Put the angled fork into the bottom dog groove first but kick the pin end out towards the case. Put the short fork in with it's pin end kicked out towards the case.
Then, put the shift drum into its hole and then rotate so some part of the grooves are towards the fork pins. Now carefully lift the angled fork up moving the drive dog along the counter shaft with it until its alignment pin will fit into its groove. Don't panic about which groove, the fork won't fit right into the wrong groove but for reference I believe the angled fork goes into the bottom groove, the short fork goes into the middle and the straight fork goes into the top. Rotate the pin end of the angled fork into until you can look down through the pin end of the fork and see the pin hole straight on. Lift the short fork and drive dog up until it's pin engages the drum and then rotate it's pin end in towards the drum. Now install the straight fork into it's drive dog and rotate it's pin end in towards the drum.
With the three forks in their places, the two fork shafts should slide down through the forks and into their repective holes in the case. Remember that the long shaft goes e-clip end up... the shorter shaft doesn't matter which end goes in first. Now, you should be looking at your bottom end with the crank, balancer shaft, two transmission shafts, three forks, shift fork pins, and shift drum sitting in there all happy and in their places. Do NOT rotate anything right now... without the skift fork pins held captive by the right side case, instead of the fork sliding along the pin, the pin can lift up out of it's hole on the left side case and fall out of the hole creating a HUGE mess of problems later.
If you lapped the cases earlier (which you should have if you pulled the crank out) make sure the right case half is clean and coat that half with sealant (grey RTV silicone or whatever your case sealant of choice is) and slide it gently over all of the shafts. The last half inch is the hardest to align and push down because the alignment pins have to be perfect and sometimes they're not perfectly round so they have to be pushed into the right side case a little bit. I have a dead blow hammer to lightly tap case halves together that are being stubborn but I do NOT recommend a hammer for someone doing this for the first time because if you're not paying attention, you could break something easily using a hammer.
Oh, make sure as you're sliding the halves together when you get close to them seating, turn the shift drum slightly to make sure the shift star points can clear the case! Otherwise the cases will never go together and you'll be standing there stratching your head wondering what's holding them apart.
The bolt tightening secquence is kinda important too.... The first screw that should be installed is the longest non-stator screw. It's the one in the very back (when the engine is in the quad) inside the stator housing. The next most important one is the short one that goes at the very top of the cases followed by the one at the bottom of the cases. Then work your way towards the end of the case jumping from the back half (transmission end) to the front (crank end) and tightening in sequence. This way, the sealant and cases are squeezed together in the middle and any misalignment between them is moved towards the outsides instead of "wrinkling" the case mating surface by forcing misalignment to the middle (kind of like doing an automobile head gasket).