focus on changing the fueling tables first (stoich, PE, etc..) Then go through and zero out some of the timing table "adders" and leave the stock Hot/Cold timing tables alone to begin with. Also, just go through the different tabs under the Engine options in HPT and anytime you see AFR or fuel, check to make sure that if there is a AFR reference/target, it is set to 9.8ish instead of the standard 14.7. That is really all there is to make sure that everything got changed! Keep us posted
Feel free to upload your tune here and I can download and take a look