I just bought a couple of used pontoons myself. I took them out to Lost lake to check them out and found quite a few things I am planning on changing. If you havent yet or are like me brand new to pontoons, take them out for a day on a lake to feel how they handle. A few things I learned on my trip, I found that on one pontoons the oars were too short for me or my friend to use effectively, need to go buy some longer ones. Will need new oar locks and an oar stops that fixes the position of the oar blades, they kept rotating on me. I also found were not to put a rod holder, still trying to figure a good place for it. I also want to sit higher and get a more comfortable seat.
My main advise is to take them out and play with them for a couple hours. It can be fun and a great way to learn what you want to modify.