I remember my 1st bike motor split too. I didn't have a service manual, was just a kid so I just tore it all apart. I had a local shop rebuild my crankshaft with a new rod kit. Putting the trans back together took me several hours. It was a trial & error gears & washers stacking exercise getting the dogs facing and meshing in the right directions and the assemblies mating up and functional with the shift drum and forks. By the time I got it all back together right I had taught myself how that trans worked though. From that day forward I felt fearless and began to split cases for other folks.
Sounds a lot like my first case split.
Mine wasn't that long ago.
Once you do one, you aren't scared of them anymore and you undoubtedly get brave and dump everything the next go round, and it takes you twice as long.
What I have learned on these transmission is, get it back together where it all spins smoothly, and rotate the shift drum while spinning the transmissions shaft to see if it will shift through all the gears and back.
Then bolt the cases back together, and do it again.
I put the wife's 420AT motor ALL The way back together and put it back in the bike, to find I'd bound the shift drum so it wouldn't shift. Had to pull the motor back out, take it all the way down again, and just loosen the crankcase bolts a hair to unbind the shift drum, then put it all back together and it worked fine.
Check and double check while putting it back together, and if you run into a hiccup, stop and ask here. It's just lego's for adults. You can do it.