Milkman
You described the problem of effecting one cylinder, then effecting the other cylinder at a later time.
I don't know how well versed you are on these bikes, but the ignition system installed, is what is referred to as the wasted spark system.
Both sparkplugs fire at the same time, so if one cylinder is effected, and not the other, it would be an ignition lead or plug. You have eliminated both of those.
The only other things that both cylinders have in common are : air intake and fuel problems.
Not trying to second guess you , but are you sure it has effected both cylinders at different times ?
When I hit reserve on the highway, I myself can't tell which cylinder is starving for fuel just by sound or 'feel', but I know the left carb has the shortest fuel line, so it will be effected first.
As Justin and airhead mentioned in their posts, I would remove the carb tops and see what you find in the way of condition of the rubber diaphragm.
After 17 years of ownership, the diaphragm on my right carb tore, and the problem ( bogging down , large hesitation, uneven running) only happened when I opened the throttle for merging onto a highway, or quickly opening the throttle.
If your carbs have not had the rubber parts replaced, this may be a good time to do it. ( Including the 'much feared' throttle shaft o-rings !)
Bing recommends that the 'needle jet' be replaced at about 25,000 miles (40,000 km), as it takes a lot of abuse from the needle.
May I suggest that you acquire some shop manuals for your bike, and before you spend a fair amount of money on a 'hopeful' fix, post here, or on some other forum that is knowledgeable on these bikes.
This might take the 'sting' out of your purchase of the ignition coil, if the coil that you removed from the bike was grey and black, you probably did yourself a favor with replacing it, as this coil has the reputation for cracking and failure. Just hopeful that the replacement OEM coil that you installed was red and black in color.
But even these upgraded replacement OEM coils are not the greatest, mine only lasted 10 years and started to give problems.
It was mentioned by either Justin, or airhead, about cleaning the screen on the fuel tap inside the tank. I can't speak about any other bike but my own, and it does not have any screen, metal or other wise on the pick-up tubes in the tank. Only filter I have from the factory, is the plastic one that threads into the fuel line fitting at the outlet of the fuel tap.
If nothing obvious is found with the carbs, airhead made a post, oh maybe 6 months ago on testing the electronic ignition control module that resides under the fuel tank. Maybe he can post that procedure ( Bill if you can, why don't you post this procedure in the Technical/ FAQ section) as I remember, it was a pretty quick non-complicated procedure. While were on the subject of the control module, remove it clean it off and apply some di-electric grease to the surface between the module and the finned heatsink. It can overheat if it can't get rid of excess heat to the heatsink, and it starts causing odd ignition problems, that go away when it cools down.
I saw in your profile, that you reside in Sydney, I don't know if corrosion is a problem in your area, but from what I have seen on living on a salt water coast, that corrosion can develop on electrical connections that are not water tight.
You may want to spend some 'quality time' with your bike, and disconnect every electrical connector, and check for the presence of corrosion by-products, white, green or rust colored ( this would include all of the frame ground points, usually a bunch of solid brown colored wires secured with one bolt or screw) and clean as necessary , apply a small amount of di-electric grease to act as a seal. Corrosion and loose electrical connections can give quite frustrating intermittent electrical problems.
