Hey Retrofan, did you manage to sort your problem out?
I think I have that same issue with my second A1200, I was thinking of trying the Anemo's Revenge trick on it. I might just get another Indi II instead though (if there are still any left available once I can afford to order a second one).
If you remove that D125 chip and just use an LED you will only get RGB output and no composite is that correct?
Is it quite easy to get yourself into a situation where you need to reflash the Indi II to get any output from it? (I'm still waiting for mine to be delivered so haven't had a chance to play with one yet).