If you get good floorboards, they will have cutouts for the foot shifter and the brake pedal and a steel piece that bolts to the top of the brake pedal, so it sticks above the level of the floorboard. I've had floorboards on several Fourtrax 300s that I've owned and liked them real well. If I had a Fourtrax 300 right now, I would buy floorboards and put on it. Although, the floorboards are probably getting harder to find now, since most of the newer ATVs already come with floorboards. I don't really see any disadvantages/negatives at all.
Most 4-wheeler problems are caused by a loose nut connecting the handlebars and the seat!!
You only need two tools in life -- WD-40 and duct tape. If it doesn't move and should, use the WD-40. If it shouldn't move and does, use the duct tape.