When my son was looking for one, all we could find were trucks that were used hard-in other words-BEAT. He ended up finding a nice truck that he liked, but had to "settle" for an automatic.
The last couple of years have been hard on our diesel's, the "ricer" crowd have discovered how simple it is to make massive power with relatively few $s. If you are purchasing a used diesel, you had better be inspecting it with a magnifying glass.
As far as "settling" for an auto trans, just be prepared to spend around $5k to bring it up to par, versus $1. 5k for a comparable clutch. I am happy with my auto trans, and would not consider a manual in it's place, but that is my preference.