Help. CEL won't go away after Engine Swap

[victoreric]

I did an engine swap to a 3.4L (from a 99') after my 2002' 2.7 died.
After the mechanical was done, it drives fine, but the Check Engine Light came on. I then got the softronic software to flash my DME and it drives better, but the CEL still won't go away. I used the intake, injectors, and MAF from my boxster. Does anyone know if I should be using the ones from the 996 and is it possible?

Does anyone else know what I can do to get rid of the CEL?

Thanks,

Eric