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I hear you - MegaSquirt seems to be a lot of money to me too. There's got to be another way at the cost of programability and versatility.
All of these electronic systems seem to be capable of adjusting to changing situations - so my guess would be that compression ratio wouldn't make a big difference. I'd be more worried about the trigger points on a crank positioning system and which other sensors would be needed for a particular system to work.
EDIT - there you go look at post #3
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