Hi Ash, welcome to the forum and congratulations on the new boat.
I have the same boat, 2004 model and if it was taken care of by the previous owner you should not have any problems with it as long as you perform proper maintenance. In fact, well cared for 4-tec engines have been known to run for over 1000 hrs without any problems. I'll try to answer your individual questions:
1: After salt water use - yes, you should flush the system with clean fresh water after use. These boats have 2 separate cooling systems, the engine has regular green coolant and a heat exchanger so it is sealed. The exhaust system uses an open water system, so that needs to be flushed after salt water use. Just hook up a hose and run it for a minute or two. Read the manual and follow instructions carefully. Start engine, turn on water, shut off water, turn off engine. Never let the water flow with the engine off b/c the engine could fill with water if you do and that would be very bad. Then you could also rinse the outside of the engine off, let it dry good and spray with WD40 as a protectant.
2: Maintenance - Again, read the owners manual and/or the shop repair manual. Basic maintenance is just like a modern car. Periodically replace engine oil and filter, change coolant, spark plugs, inspect the jet pump and make sure things are lubricated. Thats about it.
3: Hour meter - These boats do have an internal hour meter kept by the onboard computer. Unfortunately the only way to read the hours from the computer is to bring it to an authorized Seadoo dealer or buy yourself a diagnostic computer for about $400.
http://www.candoopro.com/
Starting about year 2007 they put in a digital gauge cluster that easily shows the engine hours and other entertainer information.
4: Supercharger - No, you cannot add a supercharger to this engine without a lot of work and expensive parts. The supercharged engines are set up different, different computers, injectors, etc. It is not impossible, but it would not be worth the effort. If you want supercharged then just buy a boat with a supercharged engine.
Other than that, I would recommend downloading the owners manual from BRP and download the shop manuals for your boat from this forum. Click the 'manuals' link at the top of this page. Spend some time reading and become familiar with your boat. If you have any additional detailed questions let us know. Hope this helps, and good luck!
--Deven