No, you cannot raise all of the factions in both cities. You can raise your faction with everyone in Felwithe but there are two factions in Kelethin that you will always be KOS to. If you're interested in doing whatever you can...
Kelethin
Emerald Warriors
Soldiers of Tunare
Faydark's Champions
Kelethin Merchants
Songweavers
Tunare's Scouts
Felwithe
Clerics of Tunare
Keepers of the Art*
Anti-Mage**
Merchants of Felwithe
Songweavers and Tunare's Scouts (Kelethin Bards/Rogues) cannot be raised except through quests to the guildmasters who you are KOS to. Wolf form only removes your race modifier and your Innoruuk mod will have you too low for them to accept turn-ins even if you are no longer KOS.
*Keepers of the Art, the Felwithe casters, will require you to kill Kizdean Gix in the Commonlands THOUSANDS of times which will destroy your faction with The Dead (Neriak Necro/SK guild) and Queen Cristanos Thex. There are ways to repair them, but you'll need to be strong enough to kill Dragoon Szorn in Lesser Faydark or have someone do it for you consistently while you tag him. He spawns every hour but gives +75/+100 to The Dead/Queen and -100 to King Naythox Thex. You can repair King by turning in hundreds and hundreds of Grass Woven Necklaces from halflings in Nektulos to your GM. Only Dragoon Szorn is on this faction.
Soldiers of Tunare, Faydark's Champions and Clerics of Tunare (Druids, Rangers, Clerics) are extremely easy to raise -- just invis past Pandos or be high enough for him not to attack you -- and turn in many, many WHITE wines to Lady Shae. She should be non-KOS, accept them without any prerequisites and they give the same hits as Muffins for Pandos. This will destroy Crushbone Orcs, however.
Emerald Warriors (Kelethin Warriors/Guards) are best raised by killing the Aqua Goblins in Butcherblock Mountains near the coast - NOT by killing Crushbone Orcs. Aqua Goblins will raise Emerald Warriors, Gem Choppers (Ak'Anon Warriors) and Storm Guard (Kaladim Warriors/Guard). They do not lower Indigo Brotherhood and Riptide Goblins are a KOS faction that cannot be raised anyway so there's no loss here.
Anti-Mage can be raised by turning in Bone Chips in Felwithe to the cleric GM once you have done enough White Wine. Currently there doesn't seem to be anyone on this faction but it is supposed to be the Paladin's Guild (they're all on Clerics of Tunare currently). I've been researching this and it seems that at one time not only the Paladin's guild but all of the Felwithe Guards were on this faction too... which makes sense seeing as they are pallies. At some point they were moved over to Emerald Warriors as they currently are on live. The original Alla entries still show Anti-Mage/Clerics of Tunare/King Tearis Thex as the hits for high elf guards instead of the copy-pasted hits we have now from wood elf guards. This could be fixed in the future making Anti-Mage crucial to being non-KOS in Felwithe.
Merchants of Felwithe/Kelethin Merchants are raised 'easiest' by farming shark meats. You will need a LOT of shark meat. It took me 2 weeks of farming in Erudin harbor to max my factions and I started at I believe amiable. The turn in NPC is at the Emerald Warriors guild and is on their faction... so you do this after aqua goblins.
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