yeah, i get what you're saying.

you 100% sure they are the same? they could look the same, but one could have those little silver marks on it, so double check that.

If it was my project, I'd start with the radio, and get those labeled and off to the side.
Then try to hit up the wiring diagram the best I could and get what I could labeled and off to the side.
Then, take the wires that I couldn't figure out and come up with a list of possibilities and try to eliminate it from there.
It is very possible that they cut a wire in half that they shouldn't have and that's why they had to ghetto rig things like the dash lights... so if the diagram says red with a blue stripe goes to the dash lights and something dumb like the headlight fluid, then you know that it doesn't make a stop to anything that would be where the radio is, so you could safely assume that those two wires were supposed to be connected as one wire. See what I'm saying?
That will also let you break out the multi meter to see what has power and what doesn't. That could help you figure out if the two wires were supposed to go together or not, or if one was supposed to go to something that had 12volts all of the time and the other goes to something that needs a switched 12volts. Make sense?

Start with getting what you know/can figure out labeled and out of the way, it'll make the project seem much smaller.