i just took my 2006 ford ranger 2.3l manual 5 speed wiring harness out and i went to the junk yard and found a 4x4 mountaineer 5.0l v8 1999 and pulled that wiring harness out and i put the wiring side by side and not much is matching up how might i go about that?

i can show pictures of you want

 

None of it's going to match up.

You are going to have to get the EVTM (Electrical & Vacuum Troubleshooting Manual ) You can find them on Ebay
For both your 2006 Ranger and the 1999 Mountaineer. and start matching and chasing wires.

You are going to have to figure out what wires to cut and splice, which wires you have to move pins around on the connectors,

Hopefully you also got the computer and the matching ignition keys for this 1999 Mountaineer.

Swapping in a 99 5.0 into a 2006 Ranger is going to be a wiring nightmare, most of which you will have to figure out yourself, and that's just the engine.

Then you'll have to do the same with the transmission wiring and the PATS.

You've taken on a project that probably nobody here is going to be able to help you with.