I've done a bunch of wire replacement on Mustangs and other 60's Fords. I've never used the Painless stuff,although I've heard it's good.
I typically go with the repo stuff as the quality is good(I've never had a problem) . Since I pretty much keep all my stuff period correct I like to be able to open my factory shop manual or wiring diagram and trace everything.
That said some of the repo stuff is pricey so I usually do what I can to retain main underdash harnesses.I find that that the underhood stuff gets the biggest beating 40 plus years of engine heat and exposure to the elements tends to make the wires brittle and such so I usually get new engine gauge feed harnesses and I inspect the headlight(main underhood harnesses) harnesses ,if they are bad,then I go new. Taillight harnesses I check and repair unless they are really bad. I know you have a 69 so I would double check and make sure they make the pieces you might need before tearing into anything. I'm not sure on availability on them.I rewired a 65 Fastback for a guy back in the fall (he wanted everything new repo) I think he spent $1200 or so on the parts to give an idea.
Mabcim, I hear what you're saying and I agree,If your car is pretty original and untouched your wiring is probably fine.Once again the underhood stuff usually fares the worst (the engine gauge feed,the headlight,the alternator(in your case 64 1/2 generator).
If you are worried about quailty and correctness my thought would be to ask people at shows(most restored cars have some repo wiring harnesses installed) or better yet if you are going to a big show like Carlisle ask a vendor like C.J.'s ,to bring the wiring and you can inspect it before buying.