Whats wrong with my motorcycle charging system?

For accurate results, the charging system must be checked with a fully charged battery in good condition. A weak battery may not be able to get charged over 12v No "connectivity btween" the yellow wires is not a sign of a bad rectifier, Just an improper testing procedure. A defective regulator can give the symptoms you describe. Purchase a service manual before they go out of print. It will explain the proper testing procedures.

Could be the voltage regulator

You can test your stator if you have a meter-set on continuity,put the black on a good ground and touch the red to each wire coming from the stator-if you have any continuity the stator is bad.Otherwise you can unplug it from the harness and start the bike up and measure what the ac voltage is coming out of the stator.It should be around 150 I think.If there is no continuity on that test and you have sufficient ac voltage coming from the stator,that only leaves 2 other possibilities.The rectifier or the battery.If you think the stator is good when the bike is running you should have a dc voltage reading in the high 12's at the battery post providing the battery is good also-as Jim has stated.When you throttle up the voltage should rise to a max of 14.5 or so at around 4500 rpm's or a little more,then drop back down to the low 13's-this would show the voltage regulator is working....When you start the bike,measure what the voltage drops down to when the starter is engaged-if it drops down to the 11's or 10's the battery is either junk or needs a charge.As stated a good battery is essential in solving the problem not guessing which part to change first.