I have been off the board a while trying to finish my own conversion.
Unfortunately, I can't answer the question regarding the 5 speeds in the 01-04 trucks.
I have just recently completed (if it's ever really complete) a 5.3/T56 swap into a 92 SWB truck.
I was an original 4.3/5 speed.
I bought the kit you mention from Keisler and relocated my shifter toward the center of ther T56.
I had to trim only about 1/2 inch from the original hole.
I bought a Hurst stick (I can give the part # later) and put a boot on it last night an everything looks like it was made to fit.
The shiter requires you to take part of the tranny apart, which may or may not be a big deal for you.
Hope this helps.
BTW it is a blast to drive.
'92 Fullsize, swb rc
5.3L/T56 conversion, comp XR275 HR cam .566/.568 lift 222/224 duration 112 lsa, crane dual springs, trick flow push rods, K&N Filter, Nelson Performance tune, Keisler shifter relocation kit, Boyd Coddington Smoothie II 18x8 235/55 up front, 18x10 295/45 out back, 2/4 drop, eaton lsd w/4.56 gears