hmmm.this is kinda hard without standing there and watching it..lol..all i can do is go over how i did my 2000 trx350tm rancher..maybe it will help you. with the rear lower case layed on it's side facing up..install your transmission..crank and crank shaft balencer,,make sure all your transmission gears are right..and facing the righ way..you should have your shifting drum installed also..with all these inside the case..make sure your index mark is lined up on your crank and crank balencer !!..after everything is installed..get the conecting rod up through the top of the case between the studs..if you got it all together right..the other half should just drop right down onto the one side..if not..something isn't put in the lower case right...and it's not lining up into the bearings for the top side...not sure if you have a service manual..but it sure helped me get mine back together.