I can only answer part of your question since I'm not running NYGM. I have 2 monitors though and no problems with the mod rendering (of course SH3 only runs on the main monitor).
I've also run it from the main SH3.exe and from SH3C. No problems with it.
I'm using it on top of LSH2015 right now. Sorry I couldn't be of more help.
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