As you have knackered the original drive shaft and gearbox, this is an opportunity to upgrade the last remaining part that can be a potential source of trouble.
The original design uses a system designed for surface craft. No shaft seal is present, and it relies on a grease packed stern tube to keep out the wet stuff- not the best solution for a model submarine.
What you could do is purchase a shaft system designed for sub use. The drive set-up used in the Lafayette and 212 will work perfectly in the Seawolf (similar size boat, and prop diameter). It uses a direct drive low RPM (about 5000RPM at 12 volts) 500 size motor on an aluminium mount which screws into the bulkhead, with a 4mm simmering shaft seal. The motor is fixed to the shaft with a direct coupling, and a DU bearing (bronze backed PTFE- self lubricating in water) is bonded into the stern to support the shaft at the other end.
A low friction, easy to service set-up, largely maintenance free, just add a dab of silicone oil or vaseline on the shaft seal now and again.
You may be able to reuse the existing 500, however if it is designed with a gearbox, it will probably be too high revving used direct drive.