The charging problem is simple. If you have a new stator, regulator, and battery... then there is a bad connection somewhere. Pull the connections apart, check the new parts, and give the wires at any plug a good tug. I just brought a Polaris Genesis back to life, and I found the wires in the plug, between the engine and the electrical box were all corroded. Not the plug itself (that you could see) but the wires inside the plug. Once I gave the wires a tug, they pulled right out.
The fuel prob...
OK... on a fuel injected ski... it's not easy to figure out why it's not running. As far as your test method... it's invalid. You have to leave the hoses hooked up, and put a pressure gauge on it. Just because fuel is flowing, doesn't mean there is any pressure.
Also... things like the fuel injectors may not be opening, the ECU could be bad, or your pressure regulator is bad.
The first thing to do is to see if you have any codes in the computer. If you don't... make sure the injectors are opening... then make sure you have fuel pressure.
