The onyl answer to the CEL is to imagine it says "MS on"...lol
Seriously to pass emmissions what i do is re-install the factory injectors, install the EGR and drive it on stock fuel for a few days. I disable my wastegate so the turbo cant build boost.
The factory ECU remains fully connected with the exception of the injector harness. I have tried all sorts of ways to trick the ECU that the injectors are there and none have worked.
It takes me about 1 hour to prepare for emmisions so its not bad at all really. The CEl really doesnt bother me but you could set the bulb up on a switch so you dont have to remove it to make it go away.