Don't fret too much over the compression numbers until you've got it running pretty well and for a while (200 miles with
good running, or similar distance). When the engines have this many miles they get 'unsettled' following a long sit and reawakening, which can send you down many doggie trails, chasing things that are not important, at least not just yet.
First: you've got the touchy-est 550 carbs on your hands, so anything that isn't perfect makes them act like prima-donnas. This includes (interestingly enough) the quality of the gasoline in use, and how fast it burns - or not. For starters there, use Regular gas, not Midgrade or Premium (both of these will cause run-on after throttle shutoff with today's fuels, sometimes significantly). Also add a couple of ounces of oil (any oil will do) to the gas. You've mentioned the float levels are deeper than stock for the "C" carbs, so try setting the idle screws inward a little bit, like 1/8 to 1/4 turn less than stock setting. Due partly to today's fuels, this may become your normal setting, even at the normal 12.5mm float depth (then it might be just 1/8 turn extra inward).
The spark: I have not seen coils cause this sort of trouble on a bike, but they often get blamed. Make sure the new coils are within the spec of the bike's electrics, or you'll be introducing MORE trouble, not less. The coils must be in the range of 4.3 ohms to 5.0 ohms to work well with this bike's electrics. Coils of 3 ohms WILL overload the system and leave you with chronic low-battery troubles on top of the current issues.
Next: the spark timing. Make sure the timing for both the 1-4 and 2-3 points are reaching the full-advance point, not going further. Since you can't [yet] set them at idle speeds, this will have to do for now. If possible, loosen the 3 points plate mounting screws (top one last, please) and 'dial back' a little bit of retarded timing, just a couple of degrees will do. This will help it settle back to idle speeds (and probably die, since you haven't been able to set an actual idle speed). This is a temporary diagnostic step: once the real cause of the excessive idle speed is found, you'll be moving the timing back where it belongs.
And, finally: the springs on the spark advance are not helping you now. They have become very heat-softened (we called it 'sacked') and advance the timing WAY too soon. When this is added to modern fuels that burn too slowly, the result is usually a hanging idle in the smaller Fours. So, I'd advise this as the first step (which I would do if it were in my garage today): pull the spark advancer and cut off no less than 1/2 turn from each of the advancer springs, then reinstall them and make SURE they will pull the advancer cam all the way home when released. It usually takes at least 1 full turn off 1 coil and 1/2 of the other: more often the 550 needs 1 full turn cut off both springs to make them settle well. This will retard full advance to about 2500 RPM: 3000 RPM would be much better in the end.
