I have a clymer's sitting on the shelf right above the work bench. I can tell you the head size, thread pitch, and torque spec on pretty much every nut and bolt on a blaster from memory and STILL go and refer to the manual on a regular basis. It's a helpful piece of literature.
Try pulling the crank into the left side case using the crank puller (install the 2 M8 studs into the holes provided) making SURE that the rod is hanging out of the cylinder hole (it will damage the crankshaft if it's not, don't ask me how I know!) while you're pulling it in. Once the crank is in and fully seated, you SHOULD be able to slide the right side case half on without any trouble and check to make sure that the crank is rolling over easily. Once you know the crank is going to roll over easily, you can yank the right side back off and assemble the transmission into the left side case. Apply your sealant to the right side case and slide it over. Once the right side case is down onto the locator dowels, you can sit the bottom end up straight on the bench and install and tighten case screws.
As SOON as the screws are all tightened, spin the transmission input shaft (the one the clutch goes on) and click through all of the gears. This is something the book doesn't cover but is a REAL time saver in case something is wrong in there. You can find it out now while it's easy to pull back apart versus once you've got the engine in the quad and it won't go anywhere!