Yes, the front cover was slightly longer with the earlier clutch. But lots of folks have reported that the shorter cover works OK with the early clutch. The TR6 input shaft is also somewhat shorter, so it doesn't engage as far into the pilot bearing. Doesn't seem to be a problem.
On the rear mount, the only holes I modified were the two where the mount bolts to the cross member. I drilled two new holes each about 3/8" behind the original hole (so the new hole just touched the original hole), then filed away the metal between them to form a slot. IIRC I had to bend the lip of the crossmember a bit as well, to clear the new mount position; but that may not be necessary.
I've never tried a 28% OD, but my feeling is that it might be a bit much for a stock TR motor with the stock 3.7 rear end. Taller gears mean lower rpm, but they also mean less power available (without shifting out of OD). And it's nice to have something on tap for climbing hills, changing lanes, etc. without shifting gears.
To rework Randy's table a bit (bhp numbers are from the TR2 curve in the workshop manual, but TR3 numbers should be similar at these speeds)
75 mph = 3750 rpm 1:1 80 bhp available
75 mph = 3074 rpm 1:1.22 68 bhp available
75 mph = 2930 rpm 1:1.28 64 bhp available
Also, the 22% gives an almost-perfect split between 2nd & 3rd gear; while 28% is going to move 2nd OD up much closer to 3rd direct.
Assuming the unit hasn't been tampered with, the brass tag on the OD will have the ratio marked on it in front of the model number. Eg, model 22/1374 is a 22% unit. Of course the gears can be replaced (as a set) to change the ratio, but I don't think that is very common.