If the bushing has been burnished and has the correct clearance, I can only think of two things to check.
1. Make sure the shaft is clean (no manufacturing imperfections) and is not bent and runs true. Maybe chuck the end up in a drill press and take a look at it at a low speed, see if you spot something there. A tweaked shaft will bind, either in the bushing or at the oil pump.
2. This is a stretch, but check your oil pump.
I’ve recently put together my 408 for my duster and in the process have dealt with the small block gremlins. The intermediate shaft worst of all. My problem with it is I can install it turn the motor over just fine and watch it rotate like normal however, when I try to remove it to re-clock it it will not budge. I’ve had this happen a couple of times and can’t seem to get it out without a prybar under the gear itself (big no no but I was desperate) now it’s done it again and would like some help on why it’s doing it and how to free it up without force I’ve also replaced the bushing and checked for proper clearance which it has thanks in advance!
ARP main cap fasteners have been known to be a bit too tall to clear the bottom of HV oil pumps. If the bolt immediately under the pump is contacting the pump body, when the pump is tightened down it could be distorting the pump a bit, throwing the drive a bit off kilter and causing the intermediate shaft to bind into the pump once inserted. Worth checking, but if that's not it I got nuthin' else...