hi and welcome, it looks like you may have succumed to the tedious tenere regulator fault. if you remove the reg connector check is the black wire terminal overheated or damaged in any way.
this is the most common fault, water gets in and as the terminal [i feel is too light to take the load] corrodes and overheats and fails to make the circuit, no topup voltage to the battery which steadily drains away until not enough for the ecu ,pump or ign
i recently changed mine for iirc a fz600 reg as they dont seem to have any probs and although mine was fine i have a spin to africa and dont want it to f??? up
the reg wires are facing downwards now and has done over 1k with no probs , dirt cheap on ebay as well! a simple swap over to what i feel is a more reliable setup
http://cgi.ebay.co.uk/Yamaha-FZS-600...item255d39f427 there you go!