unlike hamma mentioned above, i DO plan to move the rear axle back at some point, i want two things, less overhang and a bigger wheel well. my plan is to move the whole well back and increase the length enough to matter but not take away the stock looks of the lip or opening too much, but thats a different story and not really the point of your query so.
fender trimming really will depend on the uptravel you want, in my case i set the rig up to run 36" swampers, i did the bumpstops to just let the tires miss the roof of the well at full stuff. it was luck maybe that they fit in the uncut lips perfectly. i now run 37" PJ's and at full stuff the tires just barely rubbed the roof, i found out they were rubbing on the screws that hang down in there, once ground smooth i no longer notice rubbing. on the still uncut lips i have no rubbing on the back and just enough on the front to see the skid marks on the sliders i built, they are smooth so i dont worry about that. i would think if your bumpstops are set correctly you will be just fine with that trimming you want.