There is noway in hell a 6cyl ECU will work. 4 cyl maybe, but either way, it will need to be programable,which no std ECU are (besides WRX, EVO and LS1 V
Not sure about the whole reed valve placement thing tho. Id be trying to replicate a jetski design, as they work very well. but i'm sure they are rotory valve induction however, not reed.
Before you spend too much time on it, why not commuicate with some aftermarket ECU manufactures. Lucky AUST has he best support for this market. Microtech, Autronic, Haltech, Wolf, Motec ect.
What you are trying to achieve is definatly possibile, but unless you are a expert in EFI, have a dyno, and know the software inside and out, i dont think you'll reach your goal
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