The Microsquirt would be a likely candidate for that. I've got one here that I'm putting on my car and it's very small and would be a good replacement for the PGM if possible. You can get them from Efisource if you're serious. http://www.efisource.com/products.php?category=3

They cost a total of $400, assembled and including wiring harness! Based on the Megasquirt II, but shrunk down and missing some features. Since there are only two cylinder on the NSR it would be perfect due to it only being able to drive two coils without an external ignition, unlike the Megasquirt.

I'd say if you want to get really serious, how about developing direct injection I'm up for it.