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So the values I measured so far are: stator puts out ~39v when cranking, coil is within spec although I can't remember the exact values. The original pulse generator was 89 ohms, the new one I bought was 40 ohms and made the spark weaker somehow. So I can't rule out the pulse generator but I think you're right about the cdi.
You mentioned swapping the plug, is there a tutorial on what to do for that?
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Now that you've measured everything, the results don't mean squat. 
Seriously, electrical coils can test good, and still be bad under a load or when hot. About the only real way to test a CDI is with an actual testing unit, or on the trike, and compare it to a known good one.
Non of it is complicated, but without the tools or ability to test things in operation, resistance measurements can be very deceiving. Same with the voltage output, but it's certainly a better measurement. The pulse generator makes voltage too, that you can check.
Not trying to give you tunnel vision, but with all of my Hondas, the common failure has been the CDI. Not a single pulse coil failure, and I think one stator issue, which was on my 200ES.
To swap to the square connector CDI: From the Dr. ATV website
http://dratv.com/cdiunatseeap.html
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Great, thanks! Just bought that cdi and connector kit. I have a used cdi box coming in the mail so I'm going to see if that works, if it does work I'll keep the square connector one on the shelf for when it fails. If it doesn't work I'll swap the new box on right away
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If you didn't already know, you DO NOT have to cut wires to change the connectors. Just release the OEM wires from the connector and pop them into the new one in the correct sockets.
Go ahead and try another spark plug cap too. They're ~4k ohms. A search like ATC200ES spark plug cap on Ebay will pull some up. Choose one of the NGK ones. Caps are pretty generic for these, so you don't have to overthink it. Most of the time when they go bad, the trike just won't run, but I certainly wouldn't rule out some left field problems.
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Yeah, I thought the connectors might be the same, so I was gonna try to do that before swapping. I'll check my cap first but I might as well order a new one cause mine is cracked
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Finally got the ignition system dialed in! I don't know for sure if it was the cdi box that fixed it, or just cleaning literally every contact with sandpaper. I also ended up putting new connectors on the wires going to the cdi before swapping the plug over for the new cdi cause some of the connectors looked a bit crusty. Last things are tires, seat cover, some misc pieces for the rear rack, and a set of 200M forks cause mine are completely destroyed
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