Strange thing about connectors is... somehow they lose connection even though they are connected in the plug in's... Happened on my nitehawk, the 91 GS and a few other bikes. For no apparent reason the contact is lost... Unplug the connector and re plug it in... and its fine. In your case I'd try the ignition switch and its plug in... (BTW you happen to have a heavy key chain or some like that that may move the ket just a little and make it die, or does the key move/turn and do it by itself). Anyway check that and the other plugs under the left side cover.
Cool.
Srinath.

i brought it to school today, so far so good, its running smooth.

I only use one key (igintion key) so its not the ignition, as for teh connectors i took off a few main ones (one running from battery to fuse and a few more) and reconnected it.

As for wires on the left, where? I took out the rotor (ignition rotor) and put it back just in case that was an issue. I also took out the battery and reinstalled the screws again.

All I know the bike is running smooth (probably cause i found a few loose bolts that I tightened), its running smoother now.