To time the Dyna S you really need a timing light. Make sure you have the thing wired properly to start with. They use a black and white wire for the pickup coils but have little plastic bands on the wires (black and green) to tell you that the black band is for the 1/4 coil and green is for the 2/3 coil. Last, there is a black rotor that fits on your stock mechanical advance. This rotor has ONE magnet which provides the signal to the pickups as it rotates past the pickups. Recheck to see if the rotor is installed correctly as it will cause the ignition to misbehave if it is installed 180 degrees out. I think you put the engine at TDC for 1/4 and orient the magnet at about 9 Oclock but I would definitely recheck that with there instructions. The magnet is painted over but is an indentation about the size of a pencil eraser you can see on the outside of the rotor if you look closely... ok if the install is OK, let's look at timing the thing.
Get an inductive timing light. This means that the light is a strobe with a pickup that clips OVER a plug wire. Start the engine and warm it if you can. Timing should be done at idle but if you have to turn the idle up with the idle knob on the carbs, that is OK as you can recheck it after we are done and are able to turn the idle speed down if it doesn't want to idle at this point.
OK, engine is warm, now put the alligator clips on the battery to power the light and the inductive clip over the #4 plug wire. Loosen the 3 phillips mount screws for the plate. At idle, the mark on the case should align with the mark next to the F on your advance. If it doesn't rotate the plate till it does and once you have the marks lining up, stop the engine and tighten the three screws. 1/4 are timed.
OK, move the inductive pickup to #3 plug wire and start the engine. Essentially, the two pickups must be 180 degrees apart so the firing can take place at the right time. The timing mark next to the F for the 2/3 cylinders should line up with the mark on the case. It won't so you will need to loosen the two small screws that retain the RIGHT pickup. There are at least three small washers on the pickup and it is sometimes helpful to remove a washer on each mount screw to allow it to be moved easier. Anyway, slide the pickup coil up and down a tad and see if you can get the 2/3 F timing mark to line with the mark on the case. If you can, good; shut it down and tighten the two little socket head bolts that hold the pickup coil.
Sometimes you can't get the 2/3 timed because you run out of slot to slide the pickup coil. If this is the case, you can move the 1/4 pickup coil in the opposite direction and retime it using the same procedure as you did initally and THEN set the timing on 2/3. Remember that the pickups must be 180 away from each other and I suspect Dyna just sticks the pickup coils on any old place so the 1/4 may be towards the end of its adjustment as far as the small mount screws and may need to be moved to allow you to adjust the 2/3. Hope that made some sense. It ain't that hard once you have done it a few times.