But isn't the CFI course part of your degree plan and isn't the flight portion part of the course requirement? This is the first I have heard of this problem. The intent of the grandfathering clause was to prevent this kind of thing from happening. Have you verified all this with the VA because there is so much misinformation out there with the 9/11 GI BILL you could drive a Mack Truck through it.
I would look at any public colleges you could transfer into or find a 141 school and use your $10k/yr benefit to finish your CFI'S.