Disconnect the headlight and try it. If still no help then disconnect hood harness to eliminate the additional loads and that wiring as well.
Have you checked the crank phasing yet?
I believe you said you checked the wire harness carefully (everywhere including handlebars & tailight?), and checked the chassis ground as well as run the factory electrical tests, so I almost hate to say it if you don't have spares available, but start swapping parts, with known good ones if possible:
Ignition coil set & spark plug caps
CDI
Stator
Voltage regulators
Condenser
Carburetors
Not necessarily in that order depending on what's available to you, and I think you've already replaced some either this year or back in 2010, but maybe the replacement wasn't so good?
If you have a bud with some or all of the same parts on his good running sled, see how good of a bud he really is with his parts.

Otherwise, may have to open up the budget and find the parts, all of them are very common, or find someone with a blown or wrecked sled and clean them out. With the age of these sleds and the miles piling up, it is really, really, really nice to have spare parts laying around, and many can be found for reasonable $$.