I believe CT53541 would be a TR4A trans. They only made 40,000 or so TR4s, so CT numbers higher than that have to be 4A.
The only important difference in the transmission itself (that I know of) is that the front cover (where the throwout bearing carrier rides) got shorter by about 3/8" or so. This is required to use the 4A clutch. But supposedly the shorter cover still works fine with the TR3 clutch.
The Moss catalog shows that the 4A used the later narrow bushings for the clutch shaft; but either type will fit and work. My preference is for the earlier, wide brass bushings (and adding a way to grease them from time to time). There was also a change to the shift rail detents during TR4 production; but again either setup will work. As I recall, they changed from using a ball to a pointed plunger, which gave notchier shifts but covered up a tendency for some units to jump out of gear on overrun.
Of course, I'm comparing TR4 to TR4A. There were a whole lot of changes between TR3A and TR4, mostly to accommodate the synchromesh on first gear. Even the housing is different. If you haven't already, you'll need to elongate the holes where the rear motor mount bolts to the rear crossmember, to allow the extra length. You can force it together without slotting the holes, but the motor mounts won't last very long (BTDT).