any flashes on the dash ---> -- -- ?. was it shifting before you tore it down ?, and not now ?, or did it have a shifting problem already ?. start with getting a service manual for your atv, you should be able to down load it from the site here. second, pull the front cover off the electric shift transfer gears, and clean out all that old grease, re-pack with fresh grease, see if that helps ?. also..make sure the battery is fully charged, and in good shape ?. keep in mind, you need amps as well as 12 volts to have a good battery !. with electric shift models ?, they require a very good battery to work right.
Flashing 5 right now. Was flashing 8
you will need to down load the service manual, and in there somewhere will be the codes for those flashes, they will point you to where your problem is ?. sorry, I do not have this manual, as I only work mostly on manual shifts ( can ya guess why ?..lol ). but the codes for those flashes will help you

. worse case, it could be the angle sensor ?, or you did not line the gears up right ?, and it's messing up the angle sensor ?. that angle sensor is a high dollar part, and it must be working right ?, or it won't shift correctly at all !.