Ya take the time to think of future things and present things that need to be done on the uniframe before welding them on like transfer case skids, belly skid(if those are in your plan), cross member, E-brake bracket(if its a late model), crush sleeves for the crossmember?
I know because after specfab welded my ruffstuff ones on, we had to weld the e brake bracket on and I'm going to have to drill and tap a hole for my factory transfer case skid to fit back on.
For the front, everything that is screwed on to the front uniframe you should drill a hole for and possibly weld a nut to(like the bracket that holds your brake line)
Rear I haven't a clue on.