I swapped out my alternator and I cant seem to see where this wire goes, its red

 

is this the wire going to the plastic connector? if it is, it should go to the 12volt distribution block by your battery

 

It goes on the back of the alternator to the lug with a nut on it and plastic to isolate it from the alternator case.

 

so I'll have the battery wire as well as this to the back of the alternator?

 

this is a three wire altenator right?

if so, there should be a red heavy guage wire that goes from the threaded post on your altenator to the starter.

then there is two wires that come from the plastic connector on your altenator----the red one goes to the power distribution block next to your batttery and the other one, I believe it is tan, goes to the the ignition switch.

 

this is a two wire.

 

there is two wires that go to a plastic connector that plugs into the altenator, and a heavy guage wire that bolts to a post on the altenator right?

 

yes, I have the heavy gauge wire hooked to the battery to the post on the back of the alternator. the plastic plug that plugs has two wires one goes towards the back if the engine, probably to the fuse box. the other wire is only a few inches long and not long enough to hook up to any thing.
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and it has juice going through it

 

It goes to the same post as the battery wire like five7kid said.
I think it's the so-called sense wire, and the alt. has an internal low-ohms resistor from the sense terminal to the bat.+ post. for continued safe voltage regulation should the wire come loose. This makes it appear hot, though one shouldn't draw power from it while loose.