Sounds like your wiring conversion may not have been done properly. The ECCS relay should not be getting power until the key is in the "on" position. There should not be any power to the ECU in the "Acc" position. As you've already paid someone to do your wiring conversion, I'd suggest you contact them for support. Most reputable shops will check it as a warranty repair.
There is always the possibility that something is backfeeding power into the ECCS circuit. But if your problem started at the same time as your swap was done (and you haven't tapped wires into the harness for accessories), it's more likely to be a problem created by the guy who did your wiring.
The schematics for this engine are quite easy to find online. If you know how to use them, get a meter or a test light and check the basics. If you still have problems and the shop you paid won't help, you can contact us through our website (
www.sykoperformance.com) for instructions to send the harness in for inspection.