Just FYI, I recently obtained my father's 1991 C3500 (7.4 TBI) and I plan on installing a Santa Cruz radio. Santa Cruz offers a direct replacement for the older OBS trucks that have Bluetooth and such. looks stealthy and is modern day. https://www.retromanufacturing.com/
You could disconnect the throttle cable at the pump to ensure that the cable moves freely through it's shielding. Other than that, I think you answered your own question with the shaft difference and pull angle.
Or, you could leave it and that would keep your son from straying too far from...
I used to have issues with my battery cables coming loose and when they did the ECM (computer) would not work and the engine would have a loud rattling sound, it was timing I suspect. Once I fixed the cables it was fine. So, what I'm saying is maybe it has something do with your ECM.
Best of luck
There's not enough room for an Allison without doing at least a bodylift. I saw one a long time ago done and I recall a body lift was needed. I'll try to find the article.