Another shop experience!...
This is exactly what get me to stand on my soap box. This shop should have all the top of the line diagnostic equipment for finding this problem in the shortest amount of time possible.
As a mechanic myself and I know KustomKarl has dabbled in mechanics quite a bit himself, can tell you it doesn't take 2 hours to change out a relay, starter and battery!.....and to boot, they have equipment they use to test your battery for it's ability to hold a charge. Let's say they tested your battery and it did need to be replaced. Then after replacing, they should have been able to find out if your starter was dragging, as if it was about to go out. By your description, it sounds like your bendix isn't throwing out the starter gear like it should. Any fair weather mechanic can tell by the sound of the starter as it's being operated. Sounds like this shop may be looking to see you come back as a return customer so they can get more money!
If this was my Doo, I'd be taking this thing back and asking to talk to the manager of the shop. In my manual, I can look up the OEM recommended amount of time it takes to replace the battery, starter ect.....and I bet it wasn't that much. And they didn't fix the problem. I want my money back! If this is an OEM repair shop for Sea-Doo's and not some fly by night operation, then if you take a sensible approach when talking to the manager, letting him know you think you got the shaft, he may work with you on it. :rant:
This is only my opinion and should not be used in arbitrating your issue with the shop in question. It is an unbiased opinion, so please use it as such. But I think their jerking you around.