PCM Shows up as Ford Tarus

[KTDavis]

I have a 2003 F-250 with 7.3L that I purchased used in 2011 with 97,000 miles - one owner. It is mainly stock except for an AFE filiter system, a less restrictive muffler and an oversize Ford transmission cooler all of which I installed. I recently felt that I had transmissions problems due to slipping - RPM's increased much greater than speed. The overdrive light also flashed a couple of times. I took the truck to my local Ford dealer to check it out. He came back and told me that the truck had a custom chip and that it showes up as a Ford Tarus. He said that they could not diagnose the codes. I asked him if they could set it back to factory and he said yes but it could possible disable the PCM. He also stated that I would lose the preformance. The dealer did some test driving and said everything seemed to be preforming as it should. I did disconnect the batteries for about 30 minutes the past weekend and the truck did seem to perform as it did prior to a couple of weeks ago. So today, I took the PCM out to look for the chip. There is no chip attached. So, has the PCM been flashed? I plan to purchase a 12,000 lb. travel trailer later this year and would like to have a custom chip with a heavy tow. What should I do with the PCM in order to use the Phonix chip? Or, should I consider other options. The PCM code is PMT1. Hardware Designation is DCP-422. Part # is 1CF-12A650-ZB. Thanks for any help or advise.