I don't consider myself extremely knowledgeable on these units, but I have a 98 GSX Ltd and can comment a little on the VTS. The bellows for the VTS fails, or the clamps holding it on fail, and water goes up into the VTS motor area, which is the tear drop-shaped box when you look under the seat. Open the box (3 clips on it that must be pressed toward the box) and see how wet it is inside. First thing to do is replace the boot and get the newer design clamps so they don't cut into the boot.
The VTS also fails because the control module, made into the back of the motor box, fails due to the "pot" sealer cracking and allowing water in.
There is an aftermarket VTS controller that may be a better solution for the long term, and it is cheaper than factory parts and should be more reliable since it will be located someplace besides the back of the motor housing.
The motor can be replaced by a mid-90s Nissan passenger window motor, out of a Sentra or 300ZX, I believe. This info is searchable.
Variable Trim System Analysis
Seadoo VTS Trim Fix
Found this thread because I am also looking for answers regarding my multi-function gauge.