1. Did you gap the plugs when you changed them?
2. Could be a wiring issue I believe. What was done to the wiring?
3.once again check timing and check the coils for any cracks. Even small ones can cause it to lose spark
http://www.miataturbo.net/general-miata-chat-9/how-install-bosch-044-fuel-pump-tank-intank-56407/
Seriously read this thing top to bottom including the comments and you will shit your pants.