We just got an 06 6liter Monday. I'm not impressed :( it's supposed to be my service truck, but, I honestly would rather drive my 85 dually when pulling a machine.
Did you do anything to yours to make it less of a three legged dog?
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mine was a pulling truck, so I never had any power problem lol. as far as stock power in those, it depends who you ask...and either way, its biased most of the time anyway. ive been around quite a few and i think a lot of it is luck of the draw. some pull great, and others seem to work a little harder.
as far as preventative maintenance on the 6.0, getting an egr delete and replacing the oil cooler will help save the head gaskets. you don't need to stud the heads if you don't want to. head gasket failure on the 6.0's are more related to the egr system than the head bolts. there are silicates in the ford gold coolant. the egr cooler breaks the silicates down and gums clogs up in the oil cooler. you can stud the heads if you want to, but you want to ditch the egr first. you can also get a coolant filter kit pretty reasonable too and theyre easy to install.
as far as getting more power for towing, i recommend getting tunes from innovative diesel. they have several options with the sct programmers. when my truck was still pretty mild, i ran the sct from them that had 5 general custom tunes for the 6.0, plus 3 slots for custom tunes. with a good tow tune that 6.0 wont have any problem towing. with the sct, you can also have a turbo brake option tuned into it. theres a lot of tuning options for them, but an sct with custom tunes are by far your best and safest bet. stay away from all the edge, bully dog, etc. those will cause more harm than good