Yea for $7500 you can buy a really nice used FX HO Cruiser, or maybe 2 VXs if you shop around.........that's crazy.
The VX has Nikasil cylinders, so you basically can't re-bore, and I'm pretty sure they don't even make oversized pistons for them. Probably your cheapest alternative would be to have your head repaired and the damaged cylinder replated (I think they actually have to replate all the cylinders), piston replaced, valve repaired, etc. That would probably be around $300 - $500. There are a number of places that do that type of work, so you might want to do a search for someone near you and give them a call and tell them what you have. Here is one place that I know does PWC engines:
http://www.powersealusa.com/
Other option: From what you describe, the damage is limited to the top end, so I'm not seeing a need for a complete engine replacement. You could do a head exchange with SBT for around $500.
Both the above options are assuming that you are doing the work yourself. You would need to pull the engine, so you need a hoist, etc..
If your not mechanically inclined or don't plan to do it yourself, I'd look around for a local PWC mechanic that could do the labor. They will be much cheaper than a dealer.
If the cost gets much over $3500, I'd say you are better off parting out the ski, and buying another one.