It sounds like you are at the point of no return. It sounds like it's time to bite the bullet and make FreePBX your primary system and the Wave your alternate.
Without knowing a little more about the Wave, it's hard to help you, but here's an idea - Put a PRI card (assuming you are using PRI for the Wave) in the FreePBX server and trunk that to the Wave. That way, you can route all of the calls through FreePBX and only send to ones that need to go to the digital phones to the Wave.