Ok, the first part is to prepare your jet ski for work. If you have a special stand, put your jet ski on it. Those of us without infinite budgets must make do with the trailer. I pull my jet ski about two feet back off the back of the trailer, so the whole rear-end is exposed. Place some jack stands underneath the rear of your trailer, or the excess weight of the jet ski will tip it! I also place blocks of wood in front of and behind the wheels. This will prevent the trailer from moving while you are working on it.
I don't remember all the tools I had to use, but I will tell you this much. The screws for the ride plate and intake scoop take a #3 phillips head. Don't try a number 2. This would be fatal to all the screws, and you would have to replace them. If you have a drill with a clutch, try using this instead. (I own a 9.6v Craftsman cordless drill with a clutch, it makes short work of any screws!)
As far as extra parts you will need for the job, here they are in no particular order:
I also took this opportunity to replace all the screws with new ones from Home Depot. (our local hardware store) They carry specialty stainless steel fasteners that are a direct replacement to the stock ones.