[Brut]

You can get the Nfp pally faction up best by running into the little tavern at EFP near the gates, there's a bard standing on a table there. Give him some gold and you get faction ups with bards + pallys. There's a few militia faction guys in the bar too, but they were all green at 50 and nothing roams near enough to aggro. He takes your gold even if he's KOS. Takes a good lot of turn-ins though, so Lucan killing is also a good idea.

You can get FPMilitia faction up by doing the gnoll/orc scalp quest in Highpass. Again, you can do this even if KOS, long as the turn-in captains are green cons (which they were at 50). Couple of stacks and you should be there.

Merchants (CoalitionofTradefolk NOT CoalitionofTradefolkUnderground which is the rogue guild) is harder to raise. You can do it by either doing Rebby's Rat Whiskers, which requires some cunning tricks to do the turn-ins to the most likely kos rogue guildmaster (and a TON OF TON OF TON OF whiskers... I turned in like 10+ stacks of em and they're only threateningly). If you can hire some newbie to run em for you, go for it. Another way to get this faction up would be a quest in Erudin, where you just run around a short distance in the palace saying a phrase and turning in a potion. The hard bit with this quest ofc is that the erudites are likely to be kos, and when you do the quest, they get more kos. The guy you get the item from is a guildmaster, and there's roaming guildmasters nearby... Invis gets you around noprob, and you can do the turn-in without a hassle seeing that the turn-in guy and the fellows surrounding him are all merchants, so they won't aggro. So if you're SK/shm/warrior with cobalt greaves, this is possible - you just need to survive the inconvenient invis drops.