Does the engine run well out of gear at the full range of rpm's? If so, the problem is either The gear box, alignment, shaft or prop. There are no other possibilities. The gear box is so simple on a yanmar, I'd be very surprised if that was the problem. When you replaced the mounts, did you check for alignment? You do this with a feeler gauge at the coupling? You can adjust the alignment with the motor mount bolts. If you cant bring it in to alignment, you may have a bent shaft. Take a swim and check the prop. Your problem may be frustrating but it can be solved by moving from front to back, eliminating culprits as you go.
Good Luck!
Good Luck!