What is wrong with my cobalt?

If it is a GM stage II upgrade you might have to take it to the dealership to see if they can diagnose it. While there's any number of electronic issues that might be causing this it kind of sounds timing related. I'd take a look at the top end again. Maybe timing chain related? Did you replace the engine with another LSJ? That is the specific engine for the SS/SC Cobalt. Please let us know how this turns out. I have a stage II SS/SC as well so I'm always interested in what other people are experiencing with theirs.

I replaced it with another LSJ from a 2006 SS SC. Some of the people I work with think its a throttle position sensor issue, which makes sense. I kept the same throttle body. Also, I did timing adjustments on both engines and I know it's not that. I found out from experience that the engine won't start if the triggers aren't aligned properly (CMP/CKP) and the timing is off.

Its the car ever run good before you had the problem with the batterie? Did you replace the first engine and still does almost the same the second engine? With parts that you using from the first engine? Have you ever think that you might have a fuel problem??? Lack of fuel pressure,or just bad fuel?