500 hours is not that much for an 06 = +/- 100 hours per year which is good from my perspective as the boat has not just sat around. Lack of use is hard on machinery.
A few things to think about.
1) Review the service records.
2) Compression test (make sure you know how it is done and how Yamaha wants it done, it makes a difference). i.e. hot and WOT vs cold and throttle closed.
3) Fuel pump replacement (check for when they are due or were done 500 hours may be early for replacement)
4) Water pump impeller should be replaced every three years, more frequent if running in sandy or silty water.
5) Thermostat should be replaced with the water pump.
6) Pressure test the lower unit. Lower unit oil could have been change the day before you looked at the boat for all you know.
7) Have the computer records pulled off the engine CPU and review for how the engine was run. I would think that on 06 would have this data but not sure.
8) What do the skeg and prop look like.
9) How was the engine stored during the winter?
10) Were the engines fresh water flushed after each use in saltwater? IT MAKES A HUGE DIFFERENCE. If not pull the t-stats to get a feel for what the cooling passages look like. If clogged think about pulling a head, it is not a big deal to do.
11) Don't laugh but pull the dip stick look at the oil and then smell it. You can tell if it was over heated by smell or if any fuel has gotten into the oil it will be clear by smell. You will also pick up on additives to the oil by smell.
12) When compression testing inspect the plugs for any sign of corrosion.
13) Make sure you start the engine from a dead cold start.
Good luck.
