Ok what exactly is going on here? I know I need to replace the vacuum line from the air box (that's the only one plugged into the canister at the moment, it definitely has a bunch of holes). But where is the vacuum line that goes into the "tank" part?

1988 4.0 6cyl 2wd XJ

 

Well, on my 88 that line IS the fuel tank connection. The other goes to the air cleaner. Due to it's proximity, the "little guy" may be the line but it's hard to tell from your video. Trace it back.

 

The one I'm holding (that's not connected to anything) seems to be an electrical wire? It has 1 pin on the inside. Does that plug into the "tank" part of the canister? I would assume it would be a vacuum line correct?

 

The line to the canister is a "fuel" line since it leads back to the fuel tank. It's not under a lot of pressure so a vacuum line should works OK. That wire could be for the under hood lamp. See if it has 12v+ .