M2 stage 3 ecu and 99spec twins?
 

Will M2's stage three ecu support 99 spec turbos in addition to all the regular bolt ons? (sans midpipe)... Will it support BNR stage 3's?

maybe, the 99 twins supposedly flow more air than the < 99 stockers but the M2 ecu runs pretty rich in the higher rpms. the only way to know for sure is to slap a wideband O2 sensor on the car and find out.

I would say yes. As long as you keep it under 13psi, you should be fine. But only wideband can 100% confirm this. Could be your injectors arent flowing as much as new and that could be fatal for example.