I can't remember if the foot shift models came out with the floorboards or not, but I don't think they did. Anyway, if you don't already have them, floorboards are always a good mod. Some type of storage box is always handy and if someone rides on back with you, then a rear passenger seat/storage box is a good ideal. It makes the ride much more comfortable for the rear passenger and then you have a lot of storage room inside the seat. I would get the hard plastic kind. I have one and I love it. You can really store a lot of stuff inside one of those.
As far as the engine, I always like to leave the utility models stock. They're more dependable that way, but that's just me.