Earl,
Sorry, what do you mean by the 'pickups'? ******* I'm sorry, I tend to lapse into my habit of calling the signal generator on the crankshaft end, the pickups.......yes, I know thats incorrect

********
I'm still puzzled about the igniter unit. The Clymer manual says to remove spark plugs 3 and 4 and ground them on the cylinder head. With the ignition turned on, it says to connect the positive multimeter probe to the blue wire and the negative to the green. As the negative lead is connected, the No. 3 plug should fire and, as the negative is disconnected, the No. 4 plug should fire. That doesn't sound right to me but it is what the manual says. It also says that a 1.5 volt power source such as a dry cell battery can also be used for this test. As I understood it, this test was to simulate a pulse from the signal generator - not to check resistance.
******** The above proceedure doesnt make sense to me either. However, as you say, the purpose of the test is to simulate a pulse from the signal generator and cause the plugs to fire. That is not the purpose of the resistance test I listed for you. The purpose of the resistance test is to determine if the transistors in the ignitor box are within specified limits. If the circuits inside the ignitor box are within specs, then the box has to work properly.
There is an easy way to sort this out. The signal generator (on the crankshaft) has four wires coming from it that end in a square, four prong plug. Look at the left side signal generator and note what color the two wires going to it are. Set you meter as I said earlier and place the red test lead on one wire of the set and the black lead on the other wire of the set. Is the resistance within specs? Then check the right side signal generator pair of wires. If both sides are with the specs I gave, then there is no problem with the signal generator. (if you make this test at the four prong plug end and the results are within limits, then there can be no short or wiring problem on the signal generator side either.)
We now have two possibilities left. Either the ignitor box is not working, or the coils are not working. As you said, you have low voltage to the coils and you have too low a resistance reading on the secondaries. If the coils are not working, you can not expect even a perfect ignitor box to cause a plug to fire. You need to fix the coil problem before you will be able to do a firing test with the ignitor box.
A BTW here: yes, you can retrofit a points ignition if the ignitor box does prove to be faulty. I know the boxes are expensive. In fact, a complete, new Dyna 2000 ignition system costs less than a new replacement stock ignitor box.
Take care of the coils and verify the working of the signal generator first.
Then we can move on.
Hang in there,
Earl
I've now tried the test with the multimeter set at 200. Neither spark plug fired. If I could try the same test on a bike that I knew was working correctly then I'd be more inclined to believe the results. I've just seen the price of a new igniter unit and I really hope I don't need one. My next step is to try to find the reason for the drop in voltage at the coils.
Glad you mentioned new spark plug caps - I'd already got some more on order, though without really knowing why it was a good idea. I didn't think to check the resistance between 2 and 3 (doh - that would have required initiative!).
Roger