Have you considered going with a VQ35 instead of the VQ37VHR? Very similar and without the VVEL to worry about, and a single throttle body to simplify your air plumbing and gain more ECU options (since you mentioned the need to drive two throttle bodies). Since you are staying NA, you could even go with a VQ35DE - which I'd imagine are far more plentiful and affordable compared to a 35HR or 37VHR.
Also, Ecutek on the stock ECU seems pretty powerful for tuning... but as you mentioned there might be additional complexities introduced by trying to keep the OEM ECU. You might talk to Ecutek to see if their software can make it easier to delete a lot of unnecessary things from the loop.
It has always been a dream of mine to take on a scratch built middy project exactly as you are planning to do. Will you be documenting your build anywhere? I am a long time lurker on the locostusa.com forums, and there are a lot of really knowledgeable people there with similar projects.
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