On a TR2-4A, the bush should slide easily into the end of the crank (with the flywheel removed). Sounds like you may have gotten the wrong part(s). It seems to be distressingly common these days.
The alignment tool I got from Moss many years ago proved to be worse than useless. It's still laying in the tool chest somewhere, but I can do a better job with my finger! And as mentioned above, an old input shaft is the best possible tool for the job. My point being, don't assume the alignment tool is right until you can compare with the real thing.
Likely you know this, but JIC, the front cover on a TR3 gearbox has to be shortened by about 3/8" to work with the TR4A clutch. Otherwise, it will work when you put it together, but when you step on the clutch pedal, the fingers will try to grab the front cover. Oddly enough, they never changed the part number for the cover, but the later ones are shorter.