Are there differential drops or anything that can help with the CV issue or does the whole suspension/drivetrain need to be upgraded?
Sorry, didn't see your post originally until the OP just bumped.
With the 2nd gens apparently the CVs themselves are just fine with the angles. The main issue is the boots - at high angles the ends of the belows rub and eventually rupture - and then that can take out the CV if you don't notice it quick enough. The solution is to stretch the boots to ride further up the shaft and there are some mods to do just that. But of course that now means tinkering with yet another thing.
A diff drop is pretty much useless on a 2nd gen and potentially just makes things worse. Where the drop goes is at the front and it doesn't actually lower the diff rather it just rotates it. So the CV angles are hardly improved but now you are changing the rear pinion angle and potentially screwing up that drive line.
Keep in mind the Tacoma rear driveline is already a bit twitchy - there are TSBs for rear driveline vibes and many owners have issues. So it is kind of a roll of the dice, some people actually have a modest rear lift reduce driveline vibrations since it was originally out of spec and the lift improved the angles. Others introduce vibrations with a lift and need to do a carrier bearing drop or put angled shims on the rear axle to get things smooth again. But again, in general, you see few complaints from people at about 2" of lift. At 3" of lift plenty of people have no problems at all, but it does seem the number of issues increases.