You can move the coil packs on the back of the GN engine to the side and shove the engine even further back. Just need some custom plug wires for sure.
My RX-7 with GN power, no carpet, no passenger seat, single 3" exhaust, drag wheel combo (big/little), no spare/jack weighed 2670lbs with a 1/2 tank of gas. I had a pretty heavy Spearco intercooler, no a/c or p/s with a manual steering rack, TH200-4R and heavy D5 stall convertor.
I imagine a Miata would weigh a few hundred pounds less. You will certainly need a different rear setup. Some install 8.8" Tbird rears; however I don't know how strong they truly are. Also a rollbar to stop all the flexing from 400+ft/lbs tq from the GN6.