Yeah, this one guy I know built up a 3.4, turbo'd it and put it in a miata. only custom things he had to have done were motor mounts, a shorter driveshaft, and the hood. and for the rearend, he used a Ford 9 bolt since it bolted up perfectly. As for the engine and tranny, well, they lined up perfectly and fit like a charm. Man is that thing sick. Here's a link to his site:
http://34v6miata.tripod.com/