I'm writing this as a newbie myself to the whole auction process. I've had other mil vehicles in the past, but they've all be private purchase. I think to be armed with knowledge beforehand will save you grief down the road so I've answered your questions as well as added my .02 cents in anywhere else.
- Generally speaking, the 6.5's tend to be a little more attractive than the 6.2's. Why? Because the 6.2 is the original engine and the 6.5 isn't a unit level change out, so the truck likely went through some sort of depot rebuild at some point in it's life. Some also tend to think that it's a more powerful engine, which really is a moot point as it isn't terribly so. There are plenty of great 6.2's out there and crappy 6.5's though, so pay attention to the inspection report and videos.
- I wouldn't pay too much attention to the mileage and instead look closely at the pictures. It's well known that speedo's get swapped out with no regard for the previous mileage.
- Running vehicles go for more than non-runners because as Sandman said - it runs. This is reflected in the starting bid prices on GP - $7500 for runners vs. $5000 for non runners. I personally would stay away from anything that says "started with ether", or anything like that as that's not good for diesels. $5000 for a non runner could be something as simple as replacing missing parts - or it could mean a blown engine. I wouldn't necessarily be afraid of a vehicle that needed to be jumped, but they sell these as running vehicles with a higher starting bid price than non-runners. That's the risk you take I guess. Even a running engine is likely to require even minor work. Mine had no power steering fluid as a result of a blown hose. I replaced the hose and refilled/burped the power steering and it's running great again.
- The 4 man trucks will generally sell for more. Why? Because most folks want more than just a 2 man pickup. They want to take family/friends for rides, etc. Trucks that are more complete will sell more than incomplete trucks as it means there is less for the new buyer to likely buy. Would you want to buy 4 soft doors, a top and seats if you didn't have to? In all likelihood though, the complete trucks sell for a good bit more and the cost savings over buying one without these parts can easily mean purchasing NOS parts instead of the well used parts you'll likely get with the complete truck.
I think it's important when looking into this to do your research and to check your expectations. It's not likely that you'll get a perfect truck by any means - those that look pristine are generally selling for a very pretty penny. Those that are stripped down go for less, but need work. When I selected mine, I did it knowing that I have regular access to Humvee parts, so my highest priority was a running engine and a straight body. I paid attention to the videos posted for my particular truck and noted that it had the 6.5 in it with no blowback from what I could see. The odometer said 37K, which is probably correct for this particular engine - but again, pay no mind to it. My body needs paint - but it's straight. Mine is an M1038 and it came with the windshield, "B" pillar and 4 seats that were sunfaded and torn. It appeared to be a good running truck, so I placed my bid - and actually won it for just over the starting bid. With the exception of the Power Steering situation, the fluids all looked terrific (oil filter shows that it was last changed in November 2014) and were at the correct levels. I'm still tinkering with a few things here and there - but I really have no complaints.
While I've seen plenty of posts griping about GP, I have to say that my experience was pretty painless. They answered the phone when I called with questions and my EUC approval was in just shy of 60 days - even picking it up was painless for me with no weird hours or anything like that.
With as configurable as these trucks are, I wouldn't fret about what the configuration of the truck is that you're getting - just make sure that the condition is something that you're willing to tackle though. I'm not a mechanic, but am a good parts changer as a result of studying the tech manuals but even still have questions from time to time. It behooves you to look through the prior history of the forum and to check the manuals first as chances are it's come up before. Most are very happy to answer your questions even if you get the occasional craggy old fart that wants to tell you that it's been answered a 100x before or to study the tech manual.