Coils can be a problem in this regard. Without a coil test it can be hard to know whether a coil is actually faulty. Even then they can exibit spark at the plug but malfunction when exposed to cylinder pressures and environment and when heated during running.
Your 1-4 coil may well be faulty. But before purchasing another (used/old?) coil(s), I would swap the coil for a known good one. After all, it may not be a coil problem. If that is not practical, I'd replace with a coil(s) with removable leads (from whatever source), and preferably new. It might be more expensive but will give you better piece of mind re the ignition quality.
There are several threads in recent times discussing coil solutions. One posted today discusses the common useability of cb750/900/550 coils etc. Second hand, you take your chances. If you can get genuine parts they're probably expensive or no cheaper than aftermarket coils that (arguably) do as good a job. (Dyna 5ohm Dual Fire ?)
The important thing, is to match the coil/lead/cap to your ignition needs. Normal application for these bikes is a 5ohm coil/copper wire core leads/ 5Kohm resistor plug caps. As a general rule, don't use suppresion leads and resistor plug caps.
Beyond the coils and leads. I'd also check Hondaman's suggestion regarding the setting of the Dyna S ignition sensors/senders to eliminate that potential problem. Followed by a timing check using a timing light, on both sides of the ignition (1-4 and 2-3) independently, for idle and (say 3000rpm) advanced.
Cleaning, adjusting,cleaning,adjusting, syncing, plug chops, mixture changes etc etc. can go on forever. Once you know the ignition system is functioning properly and other normal service and tune-up items are satisfied, time spent on carburation won't be wasted.
Who knows, your carbs might be functioning pretty well, you just won't really know till your ignition is.
