I have been through this but only when I changed the waterpump. My Johnson has a control rod to change forward to neutral and then reverse. In the disassembly it is possible to not have the rod length at the required length. Adjustments are made winding the furrel end into the shift lever. Anyway on my Johnson it requires you to back out seven complete turns so the the shift works right. This may not be your problem but I thought it might be worth something. Gary