So the engine was running fine and performed well with the MSD box & coil, and you went back to the OE style setup just to pass smog? I would be inclined to go back to the MSD setup and put the OE setup back in when you need to get your smog test. Like halifaxshops said, the orange box ECU may be flaking out on you. I agree with what RRR mentioned, 25 degree advance is huge for a basically stock engine. Do you have someone with a known-good ECU that you could borrow just to eliminate the ECU being a problem?
Also the Blaster 2 coil does not need a ballast resistor. Ballast was for OE style coils and to prevent burning points, neither of which you have. You might want to try bypassing the ballast resistor to see if giving the coil the full 12v will help your issue.
