[Roger Bolick]

Yep, looks just like others I've seen. Good photos. Its a marginal clearance issue. Much better to catch it than tighten those bolts the one extra turn needed to seat that Tremec!

Machining a new transmission input shaft would NOT be my solution.

Putting a spacer anywhere in the drivetrain would NOT be my solution.

Machining the crankshaft would NOT be my solution.

Just get B50-HD bronze pilot bushing (1968 428 Mustang) and have the back side trimmed slightly, i.e. a step so as to not loose any bearing surface in the middle. Old PB can be removed with a AutoZone tool, blind bearing puller, (free with a $170 deposit) use the 2nd smallest one. Prefer the ones with a threaded shaft, but this will work. Its possible to swap this with the bell, clutch and PP in the car.

Attempt to upload rough cross section showing new pilot in original position in crank with Tremec fully seated (collides with input shaft) just tap the new PB in one more tap and you're done. (NAPA BRG B50HD $4.99, shop bill was $5, so $9.99 total)