Well lads, looks like I finally flushed out the problem... The process went something like this;
I had removed the starter some time ago but never bothered to jettison the solenoid, relay, and all the other bits related to the starter, so I started there and removed all that junk from the circuit. Took it out that morning and it ran just fine, problem solved or so I thought... confident in my assertion, I left for work in just enough time to get there.. bad call. Died on me a mile away from the house and when I looked under the seat, I found I had tripped the 20a fuse..frustrated I decided to bypass it (dumb, I know) and push on. Well, as soon as I put current through it, smoke started rising from the headlight bucket and the engine start switch.. sealing my fate and my tardiness to work. I jogged home, for the third time, and came back the next day. Ran it home straight off the battery and when I cracked it open, I found a short in the headlight bucket, among a bunch of charred wire casing, right where the flasher relay meets the engine stop switch (I had been having problems with the left signal being intermittent, so things were starting to make sense..) cut the stop switch out of the circuit and fired it up again - all was well...again, confident on my findings I set out for work the next morning only to find it running on one cylinder.. Off the tank came and that's when I saw the left coiling bulged out to all hell and everything finally came to head - I had a spare old coil laying around and after a quick swap she's been running fine ever since. A short.. a bad coil.. whatever the order, this was the cause the whole time..I suspected the coil all along but the symptoms just didn't add up..cool down made no difference and perhaps that's where the short came in.. Just thought I'd share and thanks for the help along the way