Here i am! Sorry been busy as heck here...
Ok, so it was running 100% before the swap but now it runs rough? Let me ask this, did you pull of the gas tank to get to the wiring and do the swap, or was the entire fuel system left alone? Because the fact that you have to put on the choke and full throttle sounds more like a fuel issue... But! lets troubleshoot this a bit.
Wiring i see has been confirmed, so no issues there that we know of. Those CDI's that i linked to in that post, and the one you bought, is the exact one i have on my 200ES and it runs so smooth its scary. There is no electronic advance in that unit.
Now the only suggestion i can make, other than could it be a fuel issue from tearing off the tank and possibly shaking some crud loose that got into the fuel system and the carb, is that its a bad CDI. There has been a couple guys on here that mentioned they had a CDI brand new, one of these cheap ones, that had issues. So its not impossible.
Also, check your firing timing, i know i know, it ran good with the old CDI, but who knows if someone adjusted it in the past to make it run good with that CDI that was going to crap. Set the flywheel to the F mark and then check the alignment of the advancer and the pickup, move the pickup if you need to and get the lines on them lined up. Also inspect the advancer, there is no telling if its just a coincidence that something else happened.
You can get the contacts back out of that plug, they can be released and removed and then plug the contacts back onto the pins of your original CDI, you could do that and see if it goes back to running perfect, if so then its just a bad new CDI, if not then its something else yet.
We will figure this out!
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1984 Honda ATC200ES "Big Red"
1982 ATC200E "Hondie"
1988 TRX300FW "Project Quad" Still in progress....