I'm copypasting parts of my response from the last time this topic arose, here:
http://forums.luvtruck.com/viewtopic.php?f=40&t=26741. I figure tying these types of questions together will help in the long run.
I should also preface by saying I run stock, except in places where it just makes sense to upgrade to modern hardware. The heavy-mod guys are a whole different animal (which I mean as a compliment, I swear

)
Anyhow, if you're worried about getting scammed by someone who might not be telling you the whole story, to some extent the risk you run comes down to budget. Let's say for the sake of assumption, your total budget is $1500. You should probably buy the best-running machine you can afford that
already has the situation you want. Then, expect to drop an extra few hundred bucks on minor here-and-there stuff during the first 3 months. I probably wouldn't fuss with switching transmissions unless I was prepared to spend an extra 500-1000 bucks on the swap, so first thing's first - be patient, and a little more picky than you usually are. Perhaps that means turning down a couple
almost-perfect-for-you trucks. It hurts.
Do you have any experience under the hood? Bodywork maybe? Are you good at upholstery?
For example, If you are great with (or interested in learning about) interiors in particular, you might save some cash by looking for a truck that needs what you're good at.
The flip side of this is to be extra sure not to buy something that puts you at risk of confronting what you're bad at(or can't afford!). I am no good at bodywork. It was a requirement that I find a truck with no big dents or dings. Rusty frames, floor pans, or door jambs were an instant NO-vote. Other guys on here can handle that stuff beautifully, but not me.
I bought a truck that sat in a backyard, and was in decent shape, but hadn't been run in years and needed a $30 fuel pump. Towed it home, got it running, but sure as shit, head gasket lasted about 2 miles
and I found a crack in my exhaust manifold during the teardown. Thankfully, it didn't get any worse than the crack and the gasket, but I was ready to swap a new engine into it if the problem turned out to be any deeper than that.
Most replacement engine parts are available without too much trouble. At worst, you'll have to call a few junkyards and have the part mailed to you. Cosmetic stuff is available too, but it's a bit harder to find precisely what you need. I would be surprised if you ever find a replacement dash, for instance. Don't expect to find what you need at autozone.
Lastly, speaking from experience,
It's worth the effort to take it to a mechanic, run a compression check, do a once-over on the rest of the drive train, look at the electrical situation, etc, before you buy it. Unless you're planning to drop another engine in it, don't assume all is well because it runs. If it has been sitting for a long time, expect to replace some things. The simplicity of these trucks is wonderful, but it's a double-edged sword. They were kept simple enough that joe hauler could fix things on the fly, but too often those 'quick fix' solutions are left forever. I found numerous jumped wires and cheap shortcuts after I took the time to look around carefully.
The bright side about these little trucks is that things are so basic, most repairs aren't very costly - and if you're handy, you can probably fix things yourself.
That's my take on it, anyhow.