Thanks for all your input, guys. You all rock!
@Randomroad: thanks for those tips. I used to work for a cellphone manufacturer in Chicago and initially was part of the backend (mechanical) engineering team, root-causing failures on the proto-type line, so I understand what you did and I'm applying a lot of what I learned on that job here: going through a process of elimination, but as best as I can in the 'field'
@Adv Grifter: the new stator that I installed from Procycle came with a new pickup coil and wires leading to the CDI. The problem persists even after I disconnected the stator, so I don't think it's the pickup coil. Problem persists even after I disconnected the regulator, so that's not it, either. Yeah, bummer about using second-hand donated parts, but that's what I've got here.
I did not mod my ignition switch. I'm aware of that hidden resistor and haven't touched it. All the switches on my dash (and other farkles: horn, gps, 12v socket) sit on top of the bike's harness, they plug in via a relay directly to the battery, so I dont think a short in there somewhere would cause a power loss, right?
@C/W: yup, sounds like a short to me. Going to try and replace the wiring harness when I get a chance. It's pouring down tropical thunderstorm here and no good covering to work on the bike.
@BergDonk: I checked the ignition coil connector, looks good to me. I installed my spare coil yesterday and bike was running for a bit. When this problem first surfaced, my first thought was a fuel starvation issue. I opened up the carb and saw that the float needle wasn't that smooth in its jet, so I lightly sanded the jet, got better motion for the float needle, but problem persists. What else in the carb should I look at? I have a Mikuni TM38 flat slide. I had it rebuilt before I left Nairobi and replaced the slide, float pin, air screw and reseated the float needle.
@DRT: good tip to check the fuel filter, will do.
@Multisurface Rider: good tip on cracked plug wires. I have a spare set of ignition coils with plug wires and plug caps. Problem persists with either set.
@Feelers: thanks for the that comprehensive breakdown
CDI: I have 3 on hand: original 98, take-off from a 2001 in South Africa and a good 2006 one from Arizona (installed)
Regulator: I have 2: original 98, take-off from the 2001 (installed)
Ignition coil with plug wires and caps: I have 2 sets: original 98 and 2001 (installed)
Stator: I have 2: original 98 and new 250W from Procycle with new pickup coil (installed)
I don't notice other electrical problems when it dies. I turned off the headlight, to reduce straining the battery.
I didn't bypass the neutral safety switch but did bypass the sidestand and clutch safety switches. Will check them when the rain subsides. I'll also check the handlebar kill switch.
I did replace the pickup coil as it came with the replacement stator, but I don't know if it's failed since I installed it 250 miles ago.
@heirhead: yeah, maybe the new pickup coil has failed already.