Ha.. good story Bro..

The workshop manual will tell you exactly where and which way each gear should be on it's shaft, with spacers etc, and which shift fork goes where. The cases don't have a gasket, just sealer, and I'd highly recommend you buy a tube of loctite master gasket and use.. It's clean to use and doesn't leave long strands of squeezed out silicon inside the engine to block the filters.. It doesn't really matter what gear it's in as you assemble the cases(if that was the question). As for the gear shift, I'd put the center cases together temporarily and try every gear change by turning the shift barrel from in the side case, whilst turning the two gear shafts. It would be good to have the lever and wheel in the side case that rubs on the shift barrel and holds it in each gear. That wheel both holds it in a gear once selected, but also makes sure the shift travels all the way into gear if you don't move the shift lever full travel. The shift barrel may be a little tight to turn if it's all dry in there, but you should be able to turn it with your fingers as long as you turn the shafts enough. Sometimes you will need to turn the shafts quite a few turns to allow the cogs to line up and engage, but they should all slip nicely from one gear to the next with enough turning of one or both shafts. Be patient, test it carefully up and down through all the gears. If you can get all the gears at that point, it suggests the problem is in the outer/side case, something in the shift mechanism before it gets to the shift barrel. Possibly the return spring on the lever, or the spring on the ratchet mechanism, or the ratchet mechanism itself. Post photos if it's easier than trying to describe things, or, get the manual or look things up in an online parts place, and describe parts as the book does.

Just to add to the story, it is normal on 4 stroke quad engines to have the ignition running in oil. Of course when you're used to working on 2 stroke dirt bikes usually, like I was - this may come as a surprise alright!