I believe 5sp T5's were in late production XF's. Avoid BW 0507 (5070? I can never remember) 5 sp from earlier models as can't handle 4.1.
Assuming both cars are in equivalent condition, I'd be inclined to put my money on Skyline if it had Nissan 3lt. Very good motor. Mate had one in a VL when new and it went a lot, lot better than my carb ULP 4.1 XF around same time when both cars were only a few years old. From memory Skyline sedan ran a 3.45 diff (I think VL ran 3.08) where I think manual XF's ran mainly 2.77 (my 4sp does anyway), so Skyline will still accelerate better than engine capacity suggests, but Skyline wagon may have another diff.
From memory again, ULP 4.1 EFI had about 122kw versus about 99kw in carb. When Ford dropped V8 in early '80s the EFI was claimed to accelerate as well as or better than V8 it replaced. I've driven a couple of reasonable condition stock ULP carb and EFI 4.1's lately and I've got to say the EFI, even one with about 30,000k on reco motor, was a disappointment. It's not like it's got heaps more power. I'm not sure I wouldn't just as soon have a srock Weber carb (which can flow close to Holley 350) with a decent intake manifold. Manuals (only driven 4sp single rail) definitely went better than stock auto. Auto EFI with about 170,000k on it didn't go noticeably harder than my stock carb manual with 290,000k on it. Then again it might just be that EFI's I drove were out of tune.
As for mods on 4.1 EFI or carb, effective and fairly affordable basic mods for more punch would be extractors and 2 1/2 exhaust plus 3.23 or higher diff.