What input shaft are you using in your Toploader? I ask because in my most recent build, my 4sp. fought me like no other trans ever had before regarding getting everything seated in the bell, disc and pilot. Try to put it in, pull it out, back in, pull it out. Pull the disc out, test the splines in the disc on the bench...no problem falls right on. Scat crank like yours, aftermarket big spline input but with the small block pilot tip. Only way you could get a wide ratio in a big spline, at the time.
After back and forth emails to Scat and some other checks, I am 99.44% sure that this combination is okay. I have used the same crank and input in other cars and never had an issue. Your gremlins have got me wondering all over again. Curious to hear what you find.
Mike