I did the same swap into a 2000 GT, here is the link.
T45 to T56 swap into 99-04 GT - ModularFords.com
PM me if you need more information.
I don't recall the U joints being any harder to press in then any other set I have installed.
If all else fails, you could take sandpaper (light grit) and put it around a deepwell socket that is a little smaller than the flange hole and sand lightly in a circle to enlarge it just enough to fit correctly.
Also use lubrication when installing.
Only use a vise to press them in if you have access to one.
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"Ignore that whistle, it's just a vacuum leak."
2000 Mustang GT:
Saleen Series IV Twin Screw, Chicane I/C, AFCO Extreme H/E, 2.8" pulley, FMS 42# injectors, Dual Catted 2 1/2" UPR X Pipe, UPR LCAs/UCAs, 2 1/2" Flowmaster American Thunder kit, 90mm LMAF, 112" Goodyear Gatorback, Kenne Bell BAP, Mosaleen idler, T-56, Detroit TrueTrac w/ 373s, Demolet 100mm CAI, SCT XCal2 with JDM Engineering 93 Octane "Race" tune.