Well, something's definitely wired incorrectly. I'd take a look at the FSM and the wiring diagram supplied by whoever built the MegaSquirt ECU. Those two documents should also provide enough information for you to remove the relay board. I don't know if this wiring diagram will apply to you, but here's the FSM and one possible wiring diagram:

http://www.symtechlabs.com/downloads/dl.php
http://www.symtechlabs.com/support/docs/MSWiringGuide.pdf

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-Paul

Service Manuals and Guides