Ok, more updates
Switched to Common mode, moved staging point lower, re-tuned fuel map but problem still persist.
Injector duty cycles are hitting only 70% in peak now(both primary/secondary), but ECU is still hot and after one hour of beating it, it starts shutting down injector driver.
Turning key on/off (reseting ECU) gets it back running immediately, but once higher rpm's/boost is applied, it overloads and shuts again.
Now, new idea to deal with problem :
If my problem is really caused by shutting down injector driver, i could run secondaries on external injector driver (taking the heat out of Haltech)
http://www.fjoracing.com/products/injdrvr/
I just need it here tomorrow, to try it out.