Was it a new midshaft or remanufactured? Were both midshaft and driveshaft OEM Yamaha parts or aftermarket?
If you wore the driveshaft the midshaft is shot also, they wear as a set. When you redo it with the new shaft, and midshaft, shim the pump, then put midshaft on about 1/4" away from firewall. Then use a dial indicator to check distance to firewall at all three hole locations, spin midshaft housing and recheck. Make sure they are all close to even.