As far as pistons go, most of my fl's have OEM. I do have one running with a Wiseco and it has been great over the years. I guess a lot of it depends on your useage. Some people want to ride them hardcore fast and furious. Others want to just ride them for fun. I haven't yet used a Sudco piston, but hear they are pretty decent. Call me weird, but when it comes to stuff like that, I just like OEM. But I did build the one motor with a Wiseco and it hasn't disppointed me. So there's you 3 to choose from....
Also, dunno where you got your new lower end, but rather than just trusting it, go ahead and replace both shaft bearings and seals. You will have to split the case to do this. In the long run, it could save you a heck of a lot of misery. Get all new gaskets for everything. Don't re-use any of the old ones.
In case you don't know, if any of the seals or gaskets on the motor are leaking, depending on what is leaking, it can lead to the machine not running at all, or running lean and burning it up. :shock:
I would go ahead and replace the boot for the carburator. If you're gonna do it, do it right man..... couls save you a lot of $$$$ in the long run.....