Mine was set up for a 58- 60 GM 3 speed. Then they ran 2nd and high. We chose a PG. I used a bar in the mains like you are talking about. Then we bolted it all up and it wasn't so lined up. My buddy 3dnsouth made a output shaft with a centered hub to check alignmen with. I've been adjusting with that and mounting the engine tranny with shims. Aligning like you would a coupler for pump shafts. I've got 2 58 gm 3 speeds if that would help. They are short, like 16". We went auto cause we just want to hammer and go. No clutch etc. woosed on the totally manual stuff. Then got a strange coupler for the pinion and output. Pm me if you need those trannys. They are cheap but hgard to find the short ones.