L to R 1, 2, 3, 4?
The coil the points (blue wire) aft of the crankshaft fire.
Sorry for being a dork, manual is on the way.
Exhaust
1 2 3 4
Intake
There's your cylinder order. As stated, the coils fire #1 and #4 from one coil and #2 and #3 from the other coil. So, you shouldn't be looking at your ignition for the symptoms you describe, basically. Checking your compression will be a good place to start, test the compression when the engine is warm. If you get bad compression on #2 and #4 (120 isn't 'good' as some people would like to think, above 140 would be more acceptable) squirt a small amount of oil into the cylinder and test again. If your reading goes up after that then you've got a problem with your rings, but if you still get a low reading you'll be looking at valves.
When you say it starts and idles fine until it's to temperature does it lose idle when you take the choke off?
EDIT: If you have a compression tester, but don't have that 12mm adapter or the 'universal' rubber push in type (these are kind of a hassle) here's what I did:
1) Take an old spark plug.
2) Knock off the ceramic and get the center cleared out (boy was that a pain!)
3) Find a suitable size nut and tap it to 14mmx1.25 (assuming that's the standard adapter on your compression tester) as you won't find a nut in that size otherwise.
4) Braze it to the top of the hollowed out spark plug.
5) Put it to work! It's a clever work around to paying another $15 to get the 'proper' adapter from Snap-On or similar.
