Stalling issue when coming to a stop

Yah, it could be the rotor. You might want to do a few more checks before ordering up a replacement. According to the Haynes manual, the rotor resistance should be about 5.3 ohms. Do you have a lot of confidence in the stator and other components you replaced? You may want to go back and check those again. What voltages do you get with the bike off, at idle and at 2000 rpm?
 
When measuring the resistance of the rotor there are a couple of things to do:
  1. Make sure the brushes are not in place. It is easier to access the inner ring by removing the stator assembly and of course this takes the brushes out of the equation. When replacing the stator assembly there is a small pin to align with.
  2. Check your Ohmmeter for its internal resistance by touching the two probes together firmly. My meter gives 0.9Ohm. This value needs to be subtracted from the rotor resistance reading.
  3. Place the probes firmly on the outer edge of the rings where the brushes do not contact. The rings are solf and the point on the probes will easily make an indent.
  4. Be sure the rotor has cooled to as close to 20 Celsius as possible. The reason being the specification is 5.25 Ohms +/- 10% at 20 Celsius. A hot rotor may give you a value that could be in specification.
Has someone mentioned "Weak Magnet Syndrome" if your bike still has TCI ignition fitted??? Could be causing igniton issues at low rpm. Try searching "rare earth magnet".
 
Thanks for all the feedback so far. I went ahead and replaced the rotor since everything else was new. The bike sounds a bit better but today was the first day riding and it continued to stall.
 
Still no luck, rides fine but when returning to idle just randomly cuts out. Rode the bike for about 80 miles the other day, no issues aside from the stalling once I return to idle.

I installed a new rotor, plugs, and coil, the charging system and battery are new and working properly. I went through the carbs and cleaned everything, rubber carb holders are new, checked the valve clearance and cam chain tension.

Out of ideas here, I ordered another cdi box so I'll swap that out. Is it possible I have a vacuum leak around the choke/butterfly seals on the carbs? Any other ideas are appreciated.

 
your rev counter is clearly under recording in the video. You need to ignore the rev counter and increase your idle speed until the engine doesn't cut out. I suspect that your idle is so low that the engine has insufficient vacuum to open the petcock and draw fuel from the tank so the engine is dying from lack of fuel.

Try this test . Rev the engine then close the throttle and at the moment the revs die put on a little choke and see what happens. I would guess that the engine will recover and idle due to the extra fuel
 
Pulling a plug cap with the motor running would be no problem with breaker point ignition, but it would put the igniter box at risk on a TCI system. Ground the plug cap before you remove it. 5twins developed a neat tool for this using a salvage spoke, maybe he'll chime in.
 
looking at the videos, seeing it cut out suddenly, it looks like an electrical or ignition fault of some kind. If you have purchased another TCI box, give it a try. It is possible that some of the components on the board aren’t soldered in very well and fatigue from constant vibration can cause some of the solder joints to become intermittent. However I would expect you would have problems at more than idle if that was the case. Still it is worth a try, especially if you have bought another igniter. If it is the 12 volts and ground that are intermittent going to the igniter, you could try hooking up a test light to those signals at the connector. There should be a solid voltage and ground going to the TCI box. Could also be wiring from the pickup coils or the wire going to the coil. You’ll have to check these for continuity with your meter. When you are checking the wiring, tug on it a bit while you have the meter hooked up. Does your bike have the side stand relay? If so, disconnect that relay. Given that the bike has been completely rewired, I am thinking there is dodgy connection somewhere.
 
Yes, it turns out the threads on a spoke are the same as those on top of a spark plug. That means a spoke nipple will thread right onto the top of a spark plug. Add a short length of spoke to the nipple, snap the plug cap on it, and you can run the bike. Now you can quickly and easily kill the cylinder by using a long screwdriver to ground the plug out to the cylinder fins. Grind a small groove at the top of the spoke section and the plug cap will snap on .....

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Suggested modification: use a longer section of spoke. Attach a stout aligator clamp to one end of a piece of copper core plug wire and solder the other end to the spoke. Run the nipple onto the plug by only a few threads. Attach the clamp to a cylinder fin or ground point of your choice and back the nipple off the plug--using something that's well insulated!
 
Ok so I decided to get another set of carbs. The ones I had were off a '82(?) black bs34's. I got a set of bs34's off an '80. I swapped over the jets and floats from my other set of carbs, I'm running a #45 pilot and cleaned these new carbs 2x and synced them. They are in great shape but the bike is running really lean and sounds like there's a vacuum leak. I checked the intake manifolds are tight and the vacuum line to the petcock was secure, battery is at 13.5v and so is the ignition coil. Right now the bike will only start with the choke on and riding seems like there is fuel starvation (lots of hesitation, rpms fall slowly, etc)

Is there a good way to test if there is a vacuum leak in the carbs themselves? Any other ideas?

Here is the bike idling like a lawnmower
 
Just like a lawnmower suggests running on one cylinder. If you have carb cleaner in a spray can or WD40 then spray it around the rubber where it connects on both sides of the carbs while the engine is running. An improvement in idle will indicate an air leak. When you cleaned the carbs did you check for leaks in the diaphragms after reassembly. Sometimes the diaphragm will slip out of place when the top metal cover is screwed back on.
 
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