The 2 largest PWC aftermarket performance companies are Riva Motorsports
RIVA Racing Yamaha VX110 RPM Kit and R&D Performance
R&D - Performance Kits - Yamaha - VX-110 - Performer Kit. They both offer a very basic upgrade kit for the VX that will get you 3 more mph for around $1200. They basically upgrade the impeller, ride plate, intake grate, etc., but no engine modifications (I think the Riva kit does modify the exhaust system a little).
You are right, the Magnum product is a joke. ECU modifications are possible on other skis, but not the VX, at least I've never heard of a successful attempt.
If you like the ride of the VX, my advice is to save your money, sell the VX and buy a VXR/VXS. You could easily spend the price difference on mods for your VX and still never hope to reach the stock speed of the VXR/VXS. The VXR/VXS has the same hull as the VX, but its made out of the Nanoxcel material, so its even lighter. It has an 1800 cc normally aspirated engine in it and it is kicking many of the super/turbo charged skis out there. Many more modifications are available for it now or in the works, so if you want to go faster than the stock ski speed (68 mph) you have more options.