2008 Malibu E37 Stand Alone Throttle Issues

Total Newbie here with first attempt at setting up and tuning with HPT. Having a blast screwing things up though! I have a 2008 2.4 ecotec swap out in a project Baja Offroad car. I start the engine and it either shoots up to >3000 rpm or idles rough at 800 rpm and if I touch the Pedal it shoots up to >3000 rpm. The RPM stays there but the throttle pedal does increase rpm if I press it. I pulled this motor out of a 2012 Malibu and had a bad ECM so pulled the 2008 ECM out of another car. I went to an aftermarket MAF tube that is slightly smaller than the factory and know I have to tune for that but cant get there yet. No tuning has been performed but I did remove VATS and a number of DTS's. Not sure if it is a throttle body issue. None of the accelerator position, throttle position, and or the commanded postions match and I have no idea if that is normal. I have read that manually moving the throttle plate is bad and I did do this when cleaning the throttle body before trying to start the engine. I have not been able to get the engine running well enough or stable enough to even think about tuning. I also dont know if I changed something that could have caused this.
Any input or recommendations would be greatly appreciated.

I'm not sure if this is the problem, but the 2012 2.4 engine might of had bigger injectors than the 08 ???