sounds like you changed chassis or something. That's probably the problem. I have 2 Hybrid Miatas:
Miata LS
RX-8 Renisis, racing muffler
RX-7 Infini Tires
a lot of other parts
756HP
Miata SR/Limited
911 boxer 6
Miata LS tires
RX-7 RZ intercooler
other parts
1131HP
I suggest staying with the Miata as a whole, and just changing Engine parts and stuff.
Also if you have the newest program, and you got the Miata from Change Car, it's not the whole car. You need to go to the older program and get it and save garage and read garage in the new program. I had the same problems with some cars.