FSM Auxiliary Shaft and Injector Pump Coupling

I had my engine rebuilt by a national engine rebuilder (who shall remain nameless until I find out how they resolve my problem) and when it came time to reinstall the Injector Pump, the auxiliary shaft was about a 1/4 of an inch too long and I couldn't get the pump on. When I asked the rebuilder about it they said although they knew they were longer that this was the replacement part now sold them by Ford and that they always replace them with this shaft and have never had a problem before. They advised me that I should cut off the shaft... which would be difficult since the tractor was already back together! (Who'd have thought to check the shaft length or install the injector pump before putting the tractor back together) Plus the keyways and flat on the shaft doesn't allow the coupling to go on far enough and the hole in the coupling pad is too small. I said that if this is the current replacement for the shaft then there must be something else different in the coupling and ask that he find that out for me, since obviously what I had wouldn't work! TO WHICH he replied it would be IMPOSSIBLE to find it out since Ford wouldn't have that kind of information and anyone who would wouldn't be around. So can you all do the impossible and help me resolve if there is a different coupling setup or what. So I can get this back together right...

By the way he has offered to send me a USED short shaft which I can install or if I send the engine back he'll install. Just a little inconvient!!

Thanks,
Rich