I guess I've done about as many mods to an early 99 as anyone.
I've changed the intake covers to the larger 99.5 versions
This involved getting some connector boots to adapt the old intake spyder to the larger intake diameter of the new covers. I also had to "modify" the cover on the drivers side. The higher intake cover was interfering with the bottom of the turbo's compressor housing. I "adjusted" the cover with a hammer just enough to get the minimum clearance to get the turbo mounted. You can see where the clearance was needed and how minimal it was where the little piece of cardboard is inserted.
Aside from that, I think the
Dominator 66 install, single shot injectors, Wildman flip chip, MBRP 4" exhaust, AIS w/foam sleeve, BTS trans and 6.0 intercooler are all things many others have done before.