Yep, what Travis said...

If you do want to hook the vacuum line back up, first make sure the diaphragm in the ignition box does not leak. Do the suck test. Connect a hose on the ecu vacuum port and suck on it...if you can draw air your diaphragm in the ignition box, it leaks. If so, Don’t connect the the line back to your carb.....you will be drawing in un metered air into your #2 cylinder. (Lean)
That’s probably the reason the PO disconnected the vacuum line to begin with....it leaks from a bad diaphragm.
Here you can read all about it:
http://www.fjowners.com/index.php?topic=11690.0There is no loss of performance from disconnecting this vacuum line.
Be sure to properly cap off the #2 vacuum port. Do not use cheap vacuum caps, they melt from the heat, instead use the heavy rubber oem Yamaha vacuum caps.
Hope this helps...