The basic idea behind it is that the Shadow, for a reason that will be revealed down the line and will be related to why a ta'veren is Wolfbrother and Wolf King at all, is aware that the wolves have a role to play in the LB, and it's one of Isam's tasks for the Shadow to decimate the wolves in the world, and destroy those whose souls aren't captured when killed (it's what happens when they're killed by DH, IMO) in TAR.

He had started his campaign in the Two Rivers (Perrin's homeland) before either of Fain or Perrin arrived there, which I see as confirmation that Isam wasn't hunting down Fain at the time (rather, it's Isam's report about Fain's interference with his campaign later that lead Moridin to charge Isam with also hunting and killing Fain).

This fit the pattern of Isam's campaign: originally, he emptied the mountains' area, home to most of the TR wolves (and wildlife in general, which Isam also enjoys killing). His shadowspawn, barring the occasional isolated farm (Trollocs... you can't explain much discipline from them), stayed away from people at first, especially the villages. It's rather Fain who stirred the pot by attacking farms and people) As Luc, Slayer was merely encouraging people to stay at home, not regrouping (regrouped, they might mount hunting parties) and not venturing into the wild. In short, to stay well away from him and his task of killing all the wolves.

Why start with the Two Rivers? *shrugs*. Ishamael was aware of Perrin's wolf protectors. Perhaps this had something to do with it, targeting first the wolves of his homeland. Perhaps Ishamael thought Perrin's talent was already awake in the TR and he had ties to his homeland's wolf packs. More likely, Isam simply started with an isolated area, where he wouldn't be noticed much, and from which the wolves could not easily escape. That let him bring many shadowspawn to deal with the wolves as fast as possible and then move on to a new wild area.

Further evidence Isam wasn't hunting Fain is that Fain was all the time easy to find in Watch Hill and the confrontation never came (you know, the moment Isam simply steps out of TAR and butchers Fain...). They fought each other by proxies - clearly as if neither of them was there to deal with the other, but hated the fact the other was interferring. Beside, at this point the Shadow could not be aware of Fain's real powers and if Isam needed a huge army to kill Fain, obviously Moridin would have given this task to a more competent killer later on (Cyndane, for instance). If Isam was given the task, it means Moridin thinks sending a Forsaken is overkill or a waste of their time when he has more important tasks for his two pets, and Isam is enough of a match for the likes of Fain (it's possible yet doubtful in the circumstances that Moridin has discovered Fain's merged with Mordreth. He more probably is aware of his meddling with the Shadar Logoth evil at least, as Lanfear knows about the dagger and now "tells everything" to Moridin. That would explain, because of the reaction between TP and OP that also kept him away from the Cleansing, why Moridin can't deal with Fain himself. But by his choice of Slayer, it seems Moridin still underestimates what Fain is).

The confrontation between Slayer and Perrin was "a coincidence". Oh, of course the Wheel's behind it, bringing the Hunter of Wolves and the future Wolf King into an early clash, but it's Perrin's belligerence and interference with his task which infuriated Isam and caused him to suddenly bring more and more Shadowspawn and try to scourge the Two Rivers (with result that Perrin was made into a leader, of men then, but already Faile calls him "her Wolf King", Verin speaks to him of his hammer, Alanna talks of wolves as a Shadow's bane and all but gives Perrin his wolfhead banner, and his people call him Lord Goldeneye from this point on. Ironically, the Slayer of Wolves pretty much unwittingly made Perrin take major leaps toward his future as Wolf King.

So, Isam's hordes are killing the live wolves, after which Isam hunts them and gives them the final death in TAR, so they can be reborn to enlarge the replenish the packs... when he can find them (as Hopper shows, the dead wolves are cunning enough to hide in TAR... and they do have a margin of power/control of TAR, like Dreamwalkers and all. It seems Hopper in TOM is acting again as Perrin's protector. At least, the situation Perrin was in, struggling inconsciously for control over what was taking place (but rather clearly, Perrin is no longer a complete weakling as a dreamer as he was in the first three books).. when in truth he should have full control over his own dreams, speaks a lot in favour of Cyndane interferring with Perrin's dreams as she's done before as Lanfear, but Perrin is stronger now, and Hopper remains close by.

And now for the Darkhounds...

First of all, I believe there is no "new breed" of Darkhounds. It's a red herring. Aginor is deprived of any technological means to better the breeds of Shadowspawn (beside the problem that he was already dead...). Only Shai'tan can tamper with Shadowspawn now, and there's no indication he can create a whole breed of anything at this point (it seems to take him a whole lot of effort just to have created and to maintain Shaidar Haran).

I think Lanfear flatly lied to Rand when she told him Rahvin sent the hounds to Rhuidean. She wanted Rand to eventually discover the Forsaken were allied against him, forcing him to ally with her to counter Graendal, Rahvin and Sammael.

Rahvin was going on with the plan for the confrontation in Illian, had an agent there and ready to kill Mat with an illianer dagger and really had no motive to kill Rand - and those DH clearly intended to kill Rand and Mat, and seemingly Asmodean as well. Sammael? I don't think so. Nor Graendal nor obviously Lanfear. Demandred? Probably not - that was seeking direct confrontation with the foursome, and that's not his style. Demandred wants to confront and kill Rand and - very important - for everyone to know he's done it and is the better man, not to have puppies eat him up, which would do nothing for his reknown.

I believe it's Shai'tan who sent those darkhounds (or had a Forsaken do it, who would then be immaterial), and they were linked to him directly. He saw through their eyes. It's because of their tie to Shai'tan that he was able to respawn them from a puddle of True Power from apparent death, and that only balefire could stop them. It's Shai'tan who freaked out about Asmodean's betrayal and wanted to make sure it was true, and when he saw it was true, that a Forsaken was training his enemy, he made an attempt to kill Rand and Mat. A waste of Shai'tan's efforts, as it happens. But he saw Rand knew balefire (got confirmed when he killed Rahvin), and Asmodean taught it to him it could mean he also told Rand this is the way to kill the Chosen to prevent transmigration (if he knew that...). This meant Rand could quite possibly eliminate all his Chosen before long. When a first one died by balefire at Rand's hand, Shai'tan feared the worst, immediately ordered the Chosen to back off and attempts to kill Rand were forbidden.. and he brought back the four Forsaken whose souls he held in reserve.

So... there's no new breed of DH, those two in Rhuidean were "special", being controlled directly by Shai'tan, which we now know is perfectly possible with the True Power. A new breed killed only by balefire would make it impossible for Perrin's wolves to face them... and Jordan made it clear in the late game it's the Shadowbrothers the wolves want the most badly of all shadowspawn, and started setting the table for the DH to be the most dangerous shadowspawn to Perrin, and those that as WB he should hate the most. Those wolves losing their mind and souls and turned into feral killers of their own brothers are not without thematic ties to Perrin's own struggle not to "lose himself" as a wolfbrother...

So the darkhound pack in northern Altara. I don't believe it's unique. I think it's one among many, many packs presently hunting (perhaps all the DH available are on this hunt through the world), and their quarry are all the wolves they can find and kill before Tarmon Gai'don begins (I believe new darkhounds are born by darkhound bitches killing a wolf and "eating" its soul. Their offspring then is a new darkhound. Without captured wolf soul, a bitch's offspring might rather be stillborn or something - not a true breed DH anyway). This would mean as they hunt, the pack is getting bigger and bigger (that's why the one with Perrin was said by Masuri to be unaturally big for a DH pack: it has new DH with it. A good question would be how fast Aginor has managed by tweaking genetics and using the TP to make a DH cub grow...maybe very fast...). Maybe the DH have even dealt with most of the wolves of the north by now, and only have the southern ones to deal with...

We haven't encountered more of these packs yet (we're about to in TOM, I think), because they are hunting far away from humans and normally avoid groups of humans because they aren't their targets (also, the wolves do the same and are not near humans... yet). Perrin bumped into one of them for two reasons. The first, incidental, is that Perrin's group is in the wilderness, and encountered the pack in the deep forest, away from where humans live. The second reason, why the pack circled the camp, is the presence of Elyas and Perrin with these men. Their scent as wolfbrothers confused the darkhounds, and they circled the camp before deciding to move on (they may be forbidden to attract attention). They may well have reported Perrin's whereabouts eventually - in fact I think they did just that, or will do just that in TOM... to Isam.

How will this play out? First, it appears that before (most likely, IMO) moving to the Blight eventually (his motive for moving eventually to the Blight is becoming rather obvious now...), "the hunter of wolves" is going to clash again with Perrin, whom he hates. That, the cover blurb of TOM all but told us will happen soon. The context? It seems Hopper (who acts more and more as Perrin's court fool - telling his King he is foolish) is preparing Perrin to lead the wolfpacks soon in the Last Hunt (and getting a bit desperate that Perrin isn't ready). Perrin is being kept in the wilderness by the Wheel (and learned about the "Shadowbrothers" there, no accident but the Wheel's will) and has entered his final struggle between man and wolf. He has been named Wolf King now, and carries his hammer. Perrin is also about to unite with the "wolf haters" Byar and Bornhald, who are lead by the paramount DF hater of them all: Asunawa. My theory is that everything in and around Perrin's storyline is now foreshadowing that the wolfbrother and Last Hunt stuff is soon to become the dominant element in Perrin's story (about time, some will say). I believe the gathering of the wolves (with maybe a few new wolfbrothers) to the Wolf King is about to begin, and this is the reason the Wheel is keeping its faltering Wolk King in the wilderness, multiplying the obstacles to prevent him from returning to civilization (first there was Faile's kidnapping, now there's the delay before he can use Travelling - and the delay sending home those who wish to leave will cause, and then there will be Asunawa's WC, and it looks quite possible that Maighdin will come to the forefront as Morgase not exposed by her son, but because Perrin will be her last hope to rescue Galad (yeah, it looks like we're up for another hunt and rescue storyline for Perrin.. AGAIN)... so it looks like Perrin and Byar/Bornhald and the wolves might have to put their hatred aside to work together to get rid of man who is a rabid wolf to all men (Asunawa) and free the rightful Lord Captain-Commander of the Whitecloaks....

In the meantime, the surviving wolves of the south will begin to seek their Wolf King, eventually attracting Isam and the hunting darkhound packs (a limited number of them, those converging on the gathering of the southern wolves to Perrin only. The real hordes of DH vs. wolves will be for the LB proper). Isam and his packs will be defeated or pushed back (wolves, archers, WC, Asha'man and AS) and move back to the Blight, perhaps at Moridin's orders because of the threat advancing in the Blight (mysterious, or already known by the Shadow to be Fain. we'll see). Isam's lair (his favourite one, anyway), I've long believed is at the ruins of the Seven Towers. This, in time, will position Isam for a face off with Lan (but I think this is waiting for Moiraine to rejoin Lan in the north - at the end of TOM - and finally reveal to him Isam has survived).