I'm going to try to hit the high points.
On a 2005 MCX, Perfect Pass is your only option. SG with Zbox will approximate the feel of zero off. Assuming you have the wide gauge, you can upgrade your master module, add a gps receiver, and add a zbox. Or, you can add the zbox later.
If there is a slalom course involved, speed over ground (relative to the buoys) is the only important variable. Yes, the water under the ski will feel faster with a current. But as far as scoring slalom, it is basically a timed run through the buoys, no matter what the water is doing under the ski.
For tricking, free skiing, boarding, surfing, etc., you can put PP in practice mode and manually adjust for the current. In my experience, the paddle wheel never worked all that well for holding speed. That said, if you ask PP nicely, there is apparently a version of the software that will jump over to the paddle wheel when you tell it you are in a river current. But, again, if you are in a course, not only is it not kosher, so to speak, but the pull with that paddle wheel dictating changes, is going to be absolutely horrible.
Previous: 1993 Prostar 205
Red 1998 Ski Nautique, PCM GT40, 310 hp, , Acme 4 blade, Perfect Pass SG/Zbox.
Be kind. Have fun.