Fill it up and try it out. They're pretty tough and I don't think just sitting for a few years is going to be much of a problem. I'd run it for a little bit with fresh fluid, suck out all of the fluid that you can and then run it some more. Worst case scenario is that you're about $10 worth of transmission fluid and still have to pull it and rebuild it.
As far as everything else -- you learning how things work and how to work on things now is going to save you LOTS of money in the future. Boats always need something and by fixing the small things, you'll be in a position to know what's wrong when the big things break.
Former owner of a 1987 Supra Saltare. Current owner of a Malibu 23LSV.