I am working on 06 TBSS LS2 transplanted into a 69 Camaro. It is using the 06 E40 out of the TBSS. The car was built with a 6 speed manual trans, a combo the TBSS was never equipped with. It is also using the 06 TBSS TB and pedal. The wiring harness was supplied by Speartech. I first flashed the pcm with a 06 GTO M6 file (write entire) thinking that OS might be a better match for what the car was using. That resulted in no TB movement with the pedal. Never attempted to start the car, just checked TB movement with the pedal. I knew the GTO uses a different TB but tried it anyway. So I reflashed the 06 TBSS file it originally had and the TB went back to operating normally. I wrote start up tune disabling VATS and the usual DTCs for a transplant and the car started up fine. Everything appeared to be working normal except the car would not enter PE mode correctly while driving. The Fuel System Status would change from CL-Normal to OL-accel/decel, but the commanded A/F would stay on 14.68 and the O2s would go to below 50mv. Sometimes after 4-5 seconds of commanding PE the commanded A/f would switch to to the 12.25 I was commanding in the tune, but not consistently. I've never seen anything do this before and have been doing this a long time on hundreds of vehicles. Was also setting a P0689 code, Computers and Control Systems Ignition Relay Feedback Circuit Low Voltage. The vehicle builder called John at Speartech to see if he thought anything in his harness might cause that code to set and told him about the PE problem we were having. He thought it might be because we were using a TBSS file with a M6 trans.He suggested try using a SSR calibration because a SSR was built on a Trailblazer platform and was offered with a manual trans. They also share the same TB and pedal being used in the Camaro. I didn't think that would fix the PE problem, but thought I'll give it a try if for no other reason I would be starting with a manual trans calibration. I have full M/Y licenses on 06 TBSS and have a few 05 SSRs I've licensed individually, one being a manual trans vehicle. I don't have any 06 SSR files licensed. Me thinking 05 and 06 E40s are the same, I wrote entire the 05 SSR MT file I had to the vehicle. I now have a bricked ECM. No fuel pump with key on and HPT Editor and Scanner unable to locate the ECM. Vehicle will crank but that is all it will do. Checking with my GM parts guy, he shows all 05 vehicles using E40s to be a different part # ECM than the 06 vehicles using E40s. I thought all E40s were the same. Any idea why flashing the 06 ECM with the 05 SSR cal bricked it? My guess is it has something to do with the ECM Slave modules but when I didn't brick it writing the 06 GTO file first, I didn't think writing the SSR cal would either, but it did.