06TC88,
if you do not have the Rev Xtend option then you must have older firmware installed in the Power Commander. Depending on the version you have installed you may be able to update it without needing any additional hardware.
You can read how to update the firmware here:
http://www.powercommander.com/powerc...e12.13.pdf.zip
That is a direct download to the update guide in PDF format.
The latest firmware file is here:
http://www.powercommander.com/downlo...ware_2.3.2.zip
As far as the popping, I would first check for exhaust leaks. If the file you tried made the popping worse I suspect a leak is the issue. With the way that the exhaust has been modified it is likely. Replace the exhaust gaskets as well.
Once you have updated the firmware and checked (and fixed) for leaks. Let me know if you still have an issue and we can try something else.