Running a gel battery. Specifically, what battery? Not all batteries are created equal
Tried two regulator/rectifiers Brands and models please?
Tried complete other charging system. There's a pretty simple flowchart for troubleshooting the electrical system to identify either damaged components, or faulty wiring. I use this: http://www.electrosport.com/media/pdf/fault-finding-diagram.pdf
This is killing me and any help would be great. ...And your battery apparently
A coupe of things: the 550 charging system doesn't produce a "surplus" charge until the motor is revving above ~2,500 RPMS. So, you should fire the motor, and take a voltage reading at the battery with the motor at 2,000, 3,000, 4,000 and 5,000 and record those voltages. You should see your bike charge up to 13.8-14.4v at 4-5,000.
Also, charge your battery fully. Let it rest for about 2 hours, then take a voltage reading from it with no drain. What is the voltage. Some batteries if heavily discharged, won't recover or don't recover fully. This is more applicable to Lithiums, but any battery can be damaged by repetitive discharges.
If you are encountering this "discharge" during wiring and testing, a good practice is to remove the headlight fuse so you can continue to test your system without taxing the battery. Also, what wattage headlight are you running? Many replace their stock unit with too high a wattage modern bulb and encounter exactly what you've described.
Lastly, its true the Dynatek Green coils (3 Ohms) further tax the charging system. Black (5 Ohm) coils perform better on our bikes.