Hi Sean,
a couple of things to double check:
1. check the ring gear on old vs. new. If tooth count is different you should use the starter motor that went with the original ring gear/engine. May need to swap gear.
2. if you are using a long snout starter motor ensure the transmission has a long area to accommodate it
3. you may need to ensure the steel sandwich plate fits ok
4. you may need the rubber starter motor seal, this helps the starter line up.
5. transmission lines may be coming out of left side C6, MX is right side. Even if they are the same check that the lines go to to the same general area.
6. C6 has a different kick down I think, make sure you swap that and throttle parts over too
That's about it from me, any others please chime in or amend my thoughts.
Graeme
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