Diagnosis on the rectifier. It wasnt reading anything reverse or forward.
That sounds more logical than the field coil based on the stator output, but optimistic based on the charging voltage you are seeing at the battery. If the rectifier were failed in the way you descripe (no voltage pass through) then how are you getting
any charge voltage to the battery at all?
Headlight on and around 1500 i see around 12.59 at the battery.
According to the manual you linked to in this post:
This is the manual PDF I am using...
http://www.dotheton.com/downloads/CB500-550_Manual.pdf

Your charging system is working properly at 1500 rpm. What values are you seeing at 3000 or 4000 rpm? From what I see in the manual, is that the CB550 is similar to the CB750 charging system in that they both operate at a loss below 2500 rpm (or thereabouts) and don't really start charging well until about 3000rpm. Just the nature of the beast. If your voltages are good above 3000rpm then you need to spend less time puttering around town and spend more time out on the open road "letting 'er rip".

How are you testing the rectifier? Are you using a digital meter? If so, are you using the "continuity" setting or the "ohms" setting? Many digital meters have a continuity setting because they are not sensitive enough to reliably test continuity across some diodes. The diodes only have to pass voltage one direction to convert alternating current from the "alternator" to direct current to charge the battery.
