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Carbs are Dave F modded so no brass balls.  But I'll adjust the air screw a tiny bit to see how the temp/exhaust pulse is impacted.  I was reluctant to diverge from Chuck's recommended settings so haven't tried that.

Getting back to this after work distractions and a few weeks of chilly riding through the NE and Acadia on the Guzzi.

Here's what I did, with no change in temp difference (still 30-40 degrees different):
- Re-checked timing, set at 1.9 BTDC using dial gauge, confirmed w timing light
- Checked for air leaks using starting fluid (sprayed around manifolds, spark plug hole, head gasket, base gasket) - no change in engine speed
- Measured resistance on iggy coils - both seem to be w/in spec
- Checked carb sync via the "line up mark on slide through view hole" method, handlebars pointing forward
- Confirmed both air screws set to 1.25 turns (per recommendation of Chuck after rebuilding the top end)
- Confirmed floats are set at 23mm (measured from gasket surface, with carb held sideways and float just touching the valve spring)

My gut is something is up with the left carb, or maybe there's some electrical issue.  The right (hotter) exhaust has the nice 2 stroke crackle sound; the left (colder) exhaust has more of a percussive "POP POP POP" sound.

Re the carb sync:  the Yamaha workshop manual and Haynes favor the 'lining up the slide marks' method. Others favor the 'make sure slides start moving at same time using popsicle sticks' method.  Is either one better than the other?

Re adjusting idle speed:  Haynes recommends the approach forexer explained (get running at higher than normal RPM, pull boot off right cylinder, adjust left idle screw until it feels like it's just about to die, repeat for other cylinder). Would this work if you have a crossover tube or boost bottle?  If I take off my boost bottle, plug the manifold holes and adjust using this method, would that work, or will the jetting be all screwy without the boost bottle?
                                                                                                                                                                                               

[Don't cut the P0's if you use them]

Per Dr Q:

I use 169-P2's and cut the spray shroud 1.7mm.
210's on the mains will about right.
I always start with 35 pilots on Spec II PIPES.
I'm usually also using my TSR/Barlow boost bottle/Banshee manifolds and yz125 reed petals on the stock cages.
So your on the right track. Don't cut the P0's if you use them.
5DP7--2 or 3 is good on a 2.0 airjet.

This was for a ported RD350 w JL pipes.  Someone else in the thread mentioned 2.0mm for the RD400.

http://www.2strokeworld.net/forum/index.php?topic=136.msg705#msg705

I recorded when I had to do the mod on a new carb recently and finally just uploaded it.  I didn't show the removing/re-installing of the mains/pilots/needle jet/jet needle since those are simple enough to figure out using the PDF.  The first time I did it I struggled most with the brass ball (and I still did, as shown in the video!), so I focused on that portion. Please chime in if I've mis-stated anything in the video so I can post a corrected version.

Also re-attaching the PDF

You can also reference the jetting spreadsheet to see what other people are using for their setups:

Submit your settings:
https://docs.google.com/forms/d/1jP3nMQzjXmAq-K42hHY-kwb04JnsiUc7b5Y8R_YTdEw/edit?usp=drive_web

View results: 
https://docs.google.com/spreadsheets/d/1T9KaGS9cCZbq9JfwybwA-co3t1NmSuT4D0GfrSjBrJs/edit#gid=1704700499

Forgot to mention, but I'm running the Vintage Smoke Dyna S ignition, so no points 

I recently installed some Trail Tech CHT gauges (with mount designs shamelessly ripped off from 1976RD400C's bike) to give me an objective measure of what's going on in my engine since I don't have the experience to know from feel/sound.  The left cylinder seems to be running about 30-40 degrees cooler than the right (keep in mind this is city riding, so no long straights).  Replaced the plug today and the old one was a bit oily/black. New plug runs better, but still seems like it's 4-stroking and still running colder.

Any ideas about what would cause this? Haven't had a chance to troubleshoot yet, but things that come to mind are timing, coil, ignition system generally. Battery is a Yuasa with less than 7 months on it.

Carb setup: Dave F mod, 200 main, 40 pilot, 5DP7 needle in middle

https://www.facebook.com/classic2strokes/videos/2362366170642017/UzpfSTEwMDAwNTg3NDY2MDkxMjpWSzoxNjUxMjcyNDMxNjk0MjE5/

That was easy :)  Hmm..so looks like it was stock on RD350s but they ditched it for the RD400? Wonder why. How do these dampers compare with the arm-style ones you see nowadays?

Anyone know what this grey thingy on the bottom of the triple tree is? Thinking it might be a steering damper but haven't seen one like that before.  Funny how years after owning this bike I've never noticed it before.

Bolted up these cheapy Amazon GXSR rearsets and hooked up a cheapy Amazon rear master cylinder.  They work fine for now, but let's see how they hold up in the long run.

On the SOHC forum some folks recommend using anywhere from 30,000 to 50,000 cSt silicon oil to refill the dashpot/damper pot for old CBs. Seems like it might require drilling the pot, filling with oil, then plugging the hole - assume it's similar for old Yamahas. In addition to guagerepairs.com, someone recommended Foreign Speedo, which is a company out of San Diego. Since I just got my bike running again, I'll wait until end of the riding season then send it to one of those guys after I try to fix it myself and break it.

@Striker - did you find any fix to this issue?
My speedo is also bouncing around +-10 mph or so. Cable is relatively new (maybe 3-4 years, but not many miles on it) and just cleaned out and re-lubed the speedo gear in the wheel.

Re-reading Nick's instructions for the Dyna, he says "Note: DO NOT use a screwdriver, wrench, or socket on the trigger bolt to turn the engine over. Either use the kick starter or raise the rear wheel off of the ground, put the bike in high gear, and use the rear wheel to rotate the engine. Using the trigger bolt to turn over the engine can either loosen the trigger bolt or cause a change in the timing."

So that answers that question!

Re the timing light - I'll have to order one. I'm sure this is a stupid question, but how do you actually use it? The youtube videos I watched always have a mark on a fixed point and a mark on the stator that spins.  In RDs, the stator is fully covered so there's nothing visible that spins except for the stator bolt (and the trigger that goes on it that came with the Dyna kit). So to check the timing with the light, would I (1) set the timing to 2.0 using the dial gauge, (2) put a mark on the timing plate at a position lining up with the mark on the trigger (which already has a mark on it), (3) use the timing light to make sure those marks are aligned when the light fires?

I was double checking my timing, and I noticed that the timing differed depending on whether I was turning the crank using a wrench and turning the stator bolt or pushing the kick starter.

Using the stator bolt, it was just a bit off 2.0 BTDC. Using kickstart it was about 1.7 BTDC. That seems like a not insignificant difference. I did not touch the timing plate at all in between the two checks. Note that I'm using the Vintage Smoke Dyna.

Why is that the case? Which method is the proper one for setting the timing?

See video (you have to listen for the 'snap' of the spark):

Also, just before this video I checked using the stator bolt and it was almost bang on 2.0. 1 min later, without touching the timing plate, again checking w the stator bolt, it moved to ~1.92. How in the world did it move without touching anything?