I had the clutch changed and the mechanic has got the connections to the computer screwed up. It's pumping black smoke like the choke is on - at higer RPMs enging chokes - the brake lights come on in first and second but not in 3rd or 4th or reverse. Cruise control doesn't work. He said the wires were individual and not marked. CARFAX didn't help. I think I need a wiring diagram and a way to identify each wire.

You don't have to disconnect many wires to do the clutch (reverse sw and maybe 4wd sw), and certainly not the brake lights (they're controlled by the brake pedal). And the connectors are such that you really can't connect them wrong. CC is probably not working because of the brake light problem.
You do need to get yourself a wiring diag, you may be able to download an FSM which contains them.