Alright, I'll take a crack...
These usually go together pretty easy.
First, are you sure all the gears are in the right order on the shafts?
You can put them together on the bench to make sure the gears on each shaft mesh with their partners on the other shaft and the shafts are still parallel (boats.net will also list the number of teeth on each gear if you need to check).
If you are pulling parts from multiple sources be careful about using the correct shift fork in the right place. Any chance a 465 fork from a 5-speed is in there?
Good luck, let us know how it turns out!