It is the Milodon intermediate shaft, you have to use their slightly (and I mean slightly) longer $200 shaft with that particular pump. I have filed down the edges on the intermediate a bit to no avail. I actually keep a socket and breaker bar on the crank so I can just barely bump it to see if the shaft will fall into place, it really requires two sets of hands. It truly acts like it only has one position that it will fit, so you have to have the gear in exactly the right place-maybe I'm not holding my mouth right. Cab-I am using a longer hex shaft so I can turn the pump gear. I was going to spin it over with the starter yesterday but after 30 minutes trying to get the intermediate shaft in and lined up, I just gave up and spun it with the drill. I have tried to look at everything when it does fall in so I can repeat the sequence but it never seems to work the same way twice.

Same here, I have never had the problem on any other build, but I will say that once it is in, there is very very little slop and I do like that. On my last motor the timing seemed to move around a bit when checking it, and I am now thinking between a little slop in the chain and the intermediate shaft that may have been my issue.