Kraftchick I have the same problem with my 2005 king ranch 6.0. I've got around 91k and I pull my 25' fifth wheel and have the same problems. I went ahead and added the edge evolution programmer and mbrp 4" duals straight piped/ no cat. This truck still sucks when you put it in the extreme setting. IMO this truck couldn't pull a sick whore out of bed.
My last truck was a 2006 dodge cummins and I loved the six speed and the three clutches that came with it, and the power unchipped and chipped was out of this world! However I did blow the motor in it @ 167k. They said the #6 piston broke up. This is the third out of six 05-06 dodge trucks we've replaced motors in.
Now back to the FORD- F_cked Over Rebuilt Dodge :0..... I just had the egr valve replaced, new cooler and lines, and five injectors and it still runs like crap. I feel your pain on the towing issue. A friend of mine has a 06 ford 6.0 and while he's pulling his 30' 5wheel+18' boat(pulling around 12k w/boat) I can barely keep up @65mph

pulling just my 25' weighing in at 9200.
I have had two 7.3 fords, 01 duramax, 2006 dodge and now this 2005 6.0 and have run them all right off the dealer lots and eventually into the bone yard. I work for a company that provides these trucks to us every couple of years and we run the crap out of them in the oilfield but I also use them as personal trucks so these things see every type of driving and pulling.
I can not wait to peddle this joke of a truck and I would recommend you do the same.
Oh and as far as your transmission idea I don't think thats the problem either. I just had mine replaced @ 79k.