Yep sounds very like rectifier, stick the battery on a trickle charge if you can- over night, is usually good, then start up, check the battery voltage while running it should be above 13v. if not, it's likely the troublesome connector has failed.
or disconnect the regulator connector and look to see if the black wire terminal has overheated and melted the surrounding plastic, not good! though typical for that year of bike!



checkout, http://www.xt660.com/showthread.php?t=17054 I've 46,000 on the clock most of it with this mod done, it's a simple do it and forget, really a pity yamaha did not get this right in the first place

any probs give me a shout

bernard