So, I'm in the middle of rebuilding my top end and am a little lost. There are two vacuum lines that come off the carb/manifold (S&S Super E). The line on the manifold goes to a tee, one leg goes to a vacuum switch, the other leg goes to the petcock. The second line comes off the bottom of the carb. Stock carb has similar setup. For the life of me, I can't figure out what this line is for.

 

Sounds like the second line is your overflow.

 

it might be, I was looking at it on their website. A labeled pic shows an overflow. Thank you for the response.

 

Yep it's your overflow.
As for the others I suggest you get rid of that stock petcock and get a Pingel that way all you need is one hose going to your VOES (the vacuum switch)

 

There are alternative cheaper fuel taps available similar to the vacuum one, but without the vacuum feature. You avoid problems that a vacuum tap can give, while gaining control of fuel supply. Just get into the habit of turning the tap off when parked (same applies to a fancy Pingel)!