yea...you probably should get those front bumpstops back in there if you are bottoming out. I have not experienced much rubbing of the tires on the fender flares...I would trim off the amount you need to in order to gett he sound to stop but at the same time dont trim off too much as it may start to get visible from the outside. Are you still running the stock wheel and tire combo? The reason I ask is that I havent had any rubbing until I get to full lock in a parking lot or when I am racing down the mountian and encounter a turn with a bump in it...then she rubs a bit.
You should however (as you stated) get the bumpstop brackets off the rear...it will make your ride so much more pleasant.
I also have not had any driveline vibration problems since I have installed the belltech 2" spindles and 3" angled blocks. I guess it is all going to depend on your truck(though that doesn't make sense to me, my truck is fine...yours should be too)