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Ok, here is the wiring diagram for the 1968 mustang, click here.
Give me a few minutes to look over this and think about the problem you are having. What kind of tools do you have to test? A 12 volt test light, voltmeter, etc?
I hope this makes sense. From what you are telling me you have two power feeds to the fuse box, 1 is battery power always on and 1 is powered from the ignition switch power when key on. Is that correct so far? From looking at the diagram I do see what appears to be 2 black dots I assume they are refering to as the power feed to the fuse box. Now to determine which is what, you probably have to look at what it feeds. A good hint is I know an emergency flasher can be run without the key in, so I am going to assume the spot on the lower right is battery power, then the other must be ignition on run.
I colored in the wires and shortened where they go.
I don't know why that didn't work, here click here.
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1 fuse is 14amp red/ blackgreen is + ign
2fuse is 14amp greenyellow/blkyellow is+ ign
3fuse is 2.5amp bluered/bluered is constant
4fuse is7.5amp brown/blkgreen is+ constant
5fuse is 20amp redwhite/blkyellow is+ constant
This may help.