Did you take care of your flywheel when it was off. You don't want to bump or drop a flywheel or it will mess with the magnets resulting in less power at low rpms.
Is the pickup really close to the flywheel. I don't know the spec but I make mine as close as I can get it. Maybe you have a week coil to go along with it. If it ran fine before,the weather hasn't dramatically changed and you haven't messed with anything else, it could still be electrical.
Okay, just realized you did a top end too.
Are the carbs synced, carb slides in correctly.. cutaway in slide facing airbox, choke tube in place between the carbs, float bowl with brass choke tube in it on the left carb.
disconnect the tors too, the little black box under the left side of the fuel tank.
Make sure the throttle cable is not binding or pulled where it splits under the tank.
Jetting could be a little different since you, in theory, should be pulling in more fuel and air with the rebuild.