I have a 2000 ZX202 as well and have installed a recessed foot control tray with zero issues. I have been using it for 3 years now. Measure lots so that you do not cut the hole too big! I used the aluminium tray that Bass Pro sells.
As far as seats go I have had an upholstery shop recover my seat bottoms because I wanted to keep the factory look as well as the under seat cooler and storage. I am not aware if boatseats.net are set up for folding seat bottoms or not. I think I spent $150 per seat bottom for new upholstery but they look fantastic so it was worth every penny.
Keller Williams Realty (817)713-0508