Well I got into the carbs and realized that the lemon juice was major overkill so I didn't bother. I DID go through the carb guide (thanks millions 5Twins for the manual and your patience as well as sorry for my previous redundant questions in this thread) cleaning process and made sure (as per Weekendriders suggestion) that every single hole and port was completely free and clear, and replaced any o-ring or gasket that looked even slightly worn or questionable by any measure. After reassembling and putting the carbs back on, I still had problem with the right side, as it seemed it was only firing intermittently. In addition, my idle changed and became erratic. The idle would accelerate in steps, 1100, 1200, 1300..hesitate, 1100, 1200, 1300..hesitate, 1100, etc etc. I messed with the mixture a bit again but the right side still wasn't firing properly and was bogging down like it did in the previous video I posted on YouTube.
This led me to deduce that if the carbs had been completely gone though, and the proper jets installed, the next possible issue MUST be ignition....so I dove into the points.
I've been messing with them for most of last night and most of today, and I've now got a bike that ran rough yesterday and won't start now. When it was running, I allowed it to warm up and adjusted the cam chain per the manual but I am beginning to become concerned that it may be out of spec.
I filed and cleaned the points, and adjusted the gap to .015". I found the point where they were opening by using my multimeter to check for 0 continuity by attaching one end to wire lead (from points) to the corresponding coil/cylinder and the other to ground. Doing this I found the only way I could get the top/right cylinder close to range was to rotate it CW as far as it could go. In this position I was able to get the bottom/left cylinder to open dead on the F mark of the stator, but only in the farthest CW orientation. Also, even though I tightened the cam chain when the bike was warm, I notice probably 6° of total rotational play in the cam, leading me to believe the chain is still loose.
Attached is some photos of where I ended up (I changed all the screws with allen socket heads to ease adjustment).
I've already decided I want to go with a Pamco and PMA from Hughs as I don't want this hassle again but I realize that if it's the chain nothing but replacement is going to fix that, and I'd really like to understand completely what is going on here.