Being in auto repair I'd like to throw in some thoughts.
1: you tell a customer your going to do something, you do it. AGREED
2: sometimes the customers don't know best - as the professional it's our job to educate the customer. AGREED, he knows WAY more about 6.0's than I could ever dream to know (or at least he seems to)
3: automotive repairs can't be decided on cost alone. Quality, warranty, customer service and the level of attention to detail. AGREED
4: automotive repairs time frame can't be the decider- this job couldnt, shouldn't and wouldn't be done in my shop in 3 days. Maybe I'm slow but I try to pay very close attention to every detail (and work on 50 other things a day) He said 3 days, I knew it could take a little longer. He COULD have had it done in 3 days if he would have worked on it. Both days I was there he didn't even touch it.
5: you should have absolutely verified the work when you began to question - and made it extremely clear those heads wouldn't go back on until they'd been surfaced - they can and will leak! Didn't want to piss off someone that had $14k worth of my property, when I'd have no recourse if he just quit working on it right then.
6: $1,000 less than the bill isn't exactly fair, but considering you'll likely get to do it again maybe not extremely unfair. Machine work would run 150-$300. AGREED, I felt like paying $1k less was both a great deal for me (if they never fail), and a horrible deal for me (if they do fail). For him, it covered his parts cost (about $850 or so), even covered parts he claimed to have bought (coolant and oil), and covered SOME of his time.
7: should have never picked it up until you knew it had surfaced heads on it. You have no recourse once you have paid the bill and picked it up.
Hope it works out for you! Even at $3,000 in my opinion you got a good deal! That is why I took it to him, sounded like he knew his stuff, the price ($3k) was great. I wouldn't take my excursion to someone that had not worked on 6.0's on a regular basis, but he claimed to have changed many 6.0 head gaskets. Maybe he has done so many he has found ways he feels safe cutting corners?