Does anyone know what the resistance value should be for the CT2 lighting coil. The manual does not list this, only that it should put out 5.7vac at 2500rpm to 8.5 at 8000. I am still trying to troubleshoot the engine miss with the lights on, and the only thing can find wrong is that my light coil only puts out 3.5 to 4.5vac with the light connected and on. Engine runs perfectly with the light dis-connected, but stumbles and misses above 4krpm with the light connected.
Thanks;
alnarv 

Give the points a clean & keep the gap below 15 thou. But i'm not sure on those but do think that the ignition source coil is earthed through the lighting coil, for what reason i've never worked out. But if the lighting coil is rattling around a bit in its windings & shorting the windings then it affects the ignition. Do the lights actually work when connected & look stable, not like the coil is playing up?. Had that on my HT1 & gave the points a scratch & set the gap to 14 & was good.
Starting again--i just thought, if the crank main bearing on that side is loose with easily felt up & down play then turning the lights on does something in the magnetism "I Think" & make the points gap get even worse or erratic as it pulls the crank around in bearing play.

 Make sure engine and ignition coil are grounded to frame.  Might require removing engine to sand mounting point...  especially if it was recentlypainted or powdercoated.

All of the above have been considered and addressed. This is the same bike I had previously posted about when troubleshooting a weak spark.(see post with ocilloscope pictures) It turned out to be the source coil, which measured perfectly O.K. but when put in service, would arc internally and short out the peak voltage surge to the ignition coil, limiting its secondary voltage. In the process of trying to find the problem, I replaced the points & condenser, sanded the forward mounting tabs of the engine mount, sanded the coil & bracket mounts, even pulled the stator base plate, the coils from the plate and sanded each contact point. I stripped the wire sheath to examine the wires from the stator out to the main harness, and found nothing wrong. Prior to all of this, I had suspected the crankshaft bearing play allowied the flywheel to move when the lighting coil was engaged and shifting the point gap. That turned out to be the crank journal worn down where the bearing rides. I had it welded and machined down to original spec and a new bearing installed. It is now tight as new.
On the CT2 at least, the source coil and the lighting/charging coils each ground to their respective laminate cores separately and then to the baseplate, where they become common to each other.(the only point in the system where they connect) 
I had followed a thread from 2014 where another CT2 had a similar issue. After 107 posts, the solution was reported to be: 1. cleaned motor mounts to get a good ground and 2. Retarded the timing, by "about a 1/4 inch past the original timing mark". I tried this, but using a dial guage, I found this put the timing at 0.7mm BTDC and the points at .004" gap. The bike would not even start, so I set it back to 1.8mm which set the gap to about .013", right where it should be.
This brings me back to the lighting coil. The light seems to work fine, but I have no way to determine if the brightness is where it should be as I have nothing to compare it with, except the voltage is too low. I had wondered if an internal short/ arc in the coil could somehow affect the ignition thru the ground. Has anyone ever seen this?

Do all the lights work, including the instrument bulbs? I had a CT2 that had this issue, but I rarely used the lights so I knew it was something I woud have to deal with in the future. But, I as part of regular maintenance I did 2 things, and noticed the issue with the engine breaking up with lights on was gone- 1. replaced a burnt out instrument bulb, and 2. replaced the battery (it was 3 years old and wouldn't hold a charge any longer).

 

One thing about magneto systems (besides them operating with what seem like magical powers) is that when you add load to any of the coils, it takes away from the other coils. 

Maximum ignition energy is available when the lighting and charging coils are not in use....  for example that dead battery Apex had would maximize the energy flow from the battery charge winding which would take some available energy away from the ignition. So what he said makes sense. 

Often the problem is something "marginal" like a bad ground or corroded connection which doesn't show up as an issue unless the system is pushed harder..

Points do tend to build up an invisible layer of oxidation which could be enough to cause a misfire... properly cleaning points might help.  Points system needs to be vented to atmosphere so check that too. Condenser might be breaking down too. 

Last thing to check is headlight wattage....  you said voltage is low...  these are "balanced" systems.  someone may have installed a higher wattage bulb at some point which would add lighting load and reduce ignition power slightly.  Headlight should be 25 watt....  the larger bikes had the same style light but were rated at 35 watts.

Interesting info on all lights working, I do have one of the two instrument lights out (6v 3w) and will have to replace, but I had replaced the battery a couple of weeks ago. It did the same thing before and after replacement. I have measured the charging voltages (one for day and another for night) and they both seem to put out 6-6.8v (varies with rpm) The head light is the original bulb. I have had the bike since 1978 and for most of its life I had the lights removed for use in the dirt. (it never had a battery either until a few weeks ago) The points have been cleaned multiple times (with a white business card) and the spark is solid with the headlight disconnected. When connected, I can see the firing jump all over(with timing light). It seems to shift the timing about 180deg and back intermittantly (all above about 4.5krpm)

Give the bulbs a try. I use Eiko A-62 bulbs, readily available on eBay.

Bulbs can give the 6V systems fits. A buddy's RT2 had dim lighting. We spent alot of time testing, only to find a P.O. had changed the wiring color on one instrument bulb socket (a 2 wire socket), and I had them reversed. Switched them the corect way, and restored the correct brightness to the entire lighting coil powered lights.

CT2 engine miss with lights on
As Apex suggested I replaced the burned out instrument light, no change in miss. I decided to try to video the difference using a timing light. I took 2 videos and put them together into one. The first half shows the timing with the lights on then off at real time. The second half is slowed down to apprx. 40% of normal. The shift in the firing is easier to see at a slower speed. It looks like it shifts about 180deg, very briefly then returns to normal. The angle of the camera is not straight on so the timing marks do not appear to line up but are in fact right at the indicator (1.8mm BTDC) This is the first time I have tried to add a video so not sure I got it right.

I see that the video only shows when clicking on the title in the header. Sorry!