I tested all the caps. They were 11.08k, 9.98k, 9.8k and 9.15k.
I haven't had a chance to test spark at the plugs yet. Does it matter if I test spark from the wire or should I pull each plug and ground it against the engine?
I looked for the connector at the back of the engine. The only one I saw was an 8 conductor (4x2) white plug on the rider's left side at the back of the engine case. It looked clean and firmly connected.
With a fully charged battery, I'm getting 12.51V across the battery, 11.45V from battery source to engine ground and 9.98V from battery ground to coil source. Both coil primaries are 5 ohms or less and both coil secondaries are 14.5k ohms or less.
And thanks for the help so far fellas. I'd be pulling hair out without this place.
Based on these readings, here's what you can expect to find/get:
Plug caps: I'm assuming (uh, oh...) that you have them listed as 1-2-3-4 or 4-3-2-1 in order, there: the #1-#4 pair will have weak spark on the side where the 11K cap is. Replace at least that PAIR of caps, together. NGK makes some nice-looking 10k caps for about $5 each.
The coil voltage is a bit lower than it should be: this circuit goes from the BLACK wire in the headlight to the KILL switch, then back to the headlight, then to the coils. Follow those connectors and clean each one. The KILL switch itself can have some corrosion on it, but this will actually wipe off is you operate the switch back & forth 20 or 30 times, which I do to every bike that comes by here. It's interesting how many of them end up with better RPM afterward. The voltage at the coils should be no less than 1.0 volts below battery voltage for best results (10.45 volts minimum in this case). The coils will still run down to 7.0 volts, but the engine won't rev past about 4000 RPM at this voltage.
Also, try to find the GREEN ground ring to the frame: it's either near the coils or under the seat somewhere (I forget where the 400 has it). Clean this well: it serves the whole wiring/charging system, and is equally important to the engine ground cable (did you pull that one off and scrub it clean, too? It should only drop about 0.1 volt).