Just wanted to say this forum is an incredible wealth of knowledge, even when digging back through the archives, and I hope that anyone in the future searching around finds this topic even a little bit useful 
Is there any means for you to post up some pics of your bike? Better yet, even a cell phone video? You indicate you have not tach, do you need one or do you prefer to run without one?
You stated you bought the bike form someone you trust, does he have any input or recollection of this "stumbling" while he owned it? Or was it sitting a while between being sold and bought by you? If so, very necessary to also check the fuel supply for debris that may be obstructing your carbs.
I know you said the carbs were cleaned, but can you provide some specifics about who/how/when they were cleaned? Did you remove and fully clean the emulsion tubes? Area the floats set properly?
I ran though the fuel system first, as it is easier (for me personally) to pragmatically diagnose than electronics (ex: inspect/clean inline filters, tank pickup, petcock, carb emulsion tubes, jets, slide needles) and I can say with confidence the parts are newer, with good seals, and are very clean.)
I'm now working on trying to diagnose if it's the coils, dyna ignition, or both. Two more questions for 50 points each!
1: I found how to test out coils in the FAQ (http://forums.sohc4.net/index.php?topic=5752.msg8383#msg8383),
but I can't seem to find a procedure to test out the Dyna S itself. Anyone have any idea how to test it?
Also, since I'm having the problems when the motor is hot, do I have to run these tests during/right after a ride, or can they be ran when cool?
2: I'm looking at picking up the PAMCO ignition, and was debating between just getting the ignition and using the stock coils I have, or getting the package that comes with the "cool running coils increase the MPG by 5.20%" (http://www.allcyclesupply.com/product/ACS-31168).
Does anyone know what the resistance on these coils are? 3 or 5 ohms? I just want to make sure I don't induce any more drain on the poor charging system than it already has... :\
One of the problems that crops up with the Dyna S involves the gap spacing between the magnet (in the spinning advancer cam) and the pickups' face. These often get set unevenly if someone just plunks in the baseplate and tries to use Dyna's 'static timing' routine. In this regard, Dyna's instructions could be clearer?
Here's the skinny on it: the triggers themselves are Hall Effect electronic switches. In this type, they are turned ON all the time until the magnet passes close by: then they switch OFF while the magnet is within detection distance. When they switch OFF, it simulates the points opening, so the coil loses the current that was passing through, and its magnetic field collapses to produce the spark (much like points' actions).
Now, here's the tricky part: the field strength of the little magnet they use is not super strong. So, it must be set at a close distance to the trigger to make it switch ON. If it is TOO close, it will not switch ON, if too far away, it will not switch ON, and if not in the "optimal" distance, will switch on late or early, compared to where it should be set. There is a fairly narrow range where they operate correctly, but once set in this range, they usually do well.
When the Hall Effect devices heat up (with the engine) their characteristic changes slightly, making them act somewhat differently when the magnet comes near. If the gap is too small and the magnet comes too close, the switch turns ON sooner when hot, as compared to the cold setting, causing excessive timing advance. Vice-versa when the magnet is too far away: it will trigger, but it will be "late" and the timing will be retarded, or (more often) the spark will be weak. In both cases (too close or too far away), the undesired effect shows up better (i.e., more completely) when hot. It will act differently when cold, so setting it cold is problematic with Dyna S, and has been since they were introduced in the 1970s. Sadly, their instructions usually have you set them up cold.
So...early on, we learned to warm up then engines with the Dyna installed, THEN adjust them for timing using only a strobe timing light for best speed (those of you old enough to remember the old, slow orange neon timing lights know what I'm getting at, here...). And, the gaps between the L and R pickup MUST be the SAME, or one side will vary compared to the other as the engine goes through temperature changes.
The Dyna S has had 3 different "gap specs" that I am aware of: the earliest ones (with a blue PC board base) were .020"-.025" gaps. The later ones (with the PC-board base, but in tan or whitish color) were at first said to be .015"-.020", later were changed to be .020"-.030" spec. The latest versions that I know about are the ones with the large, metal-clad pickups with nylock nuts that hold them to the baseplate: the spec I have most often heard for these is .025" (no lo-hi range given).
If the gaps are not even, then the timing will also not be even. Sometimes you will see reports in the forums where someone finds they cannot adjust them (or maybe just one side) to slow down for idle, or else if they set it to idle position it will not reach full advance when revved up. In a few cases, this has been the fault of the little cam with the magnet, which got dirty, stuck, or made wrong, and it doesn't rotate like it should with the advancer unit. In most cases, it has been either incorrect gap(s), or a failing trigger(s) on the unit.
The most common outright failure mode we have observed for the last version (with the metal-clad triggers) has been where a trigger fails when hot. The failure is this: the device turns ON but refuses to turn OFF enough when the magnet passes by, so the spark is weak or non-existent during the "spark time". If you scan back through the last 5 years on these forums, this is the failure mode you will most find.
For the most part, the Dyna S has been a pretty good replacement for the casual rider of the SOHC4 bikes, if the rider was not overly concerned with the bike's performance. Above 6000 RPM, the spark duration is quite short because the OFF time of the trigger is less than the spark duration of the stock Honda coils (or the 5 ohm Dyna coils). This leads to slightly less HP at higher RPM as compared to points performance. On the 750, few riders notice this difference as that RPM is above most posted speed limits, but on the smaller bikes it has long been noticed.
