I watched your video of it running and stalling.
Is that gas (fuel) hose between the aftermarket-installed inline filter and carburetor folded flat at all at its downward turn bend and restricting gas flow to the carb ?
Have you verified a steady stream of gas coming out of the fuel hose from the inline filter when the tank's petcock is open ?
To verify mine, I removed the gas hose from the carb inlet, aimed it into a clean glass bottle, opened the petcock and watched. If it is only a slow trickle or is only dripping out, then you've got bonafide flow restriction and there are several possible causes :
1) Tank's fill cap's vent is clogged - blow the cap's vent hole(s) clean with an air compressor blow nozzle or boil the cap clean in boiling water
2) Tank's in-tank filter (if it is still there and you or a previous owner have not already removed it from inside of the tank) is clogged or partially clogged - drain the tank enough so you can remove the petcock from the tank and then remove the tank filter tube and clean it - it's a plastic tube with a very fine mesh screen that runs nearly the entire height of the tube -
IF it does not come out with the petcock's rigid plastic tube when you remove the petcock, nor if it does not come out when GENTLY inserting a sufficiently-sized bolt or screw or a tapered flathead screwdriver into the filter tube
so to help twist the filter tube out of the tank, THEN GENTLY INSERT (by hand-screwing) a large "Eazy-Out" bit into the filter tube so the spiraled teeth of the Easy-Out grip the tube and then twist it out of the tank so to inspect it and clean it if the mesh screening is still fully intact. You can see both an illustration of and an actual color photo of the petcock, its rigid plastic tube and semi-rigid filter tube screen here
Honda 16950-385-701 - PETCOCK ASSY. | Partzilla.com
By the way, the mesh screening of the in-tank filter tube is so fine that you do not need that aftermarket inline filter showing installed between your tank's petcock and your carburetors in the video. Besides, when the plastic of that inline filter cracks apart, it could leak gas straight downward onto the left-side exhaust pipe or muffler or even onto the "power chamber" between the left and right side exhausts and start a fire or worse...
3) the aftermarket inline gas filter between the petcock and carburetor is clogged dirty or partially clogged, sufficiently restricting gas flow
4) and with that inline filter installed and occupying hose line space, the hose downstream of it is having to make so much of a bend to the carb, that it is actually folding tight (especially when exposed to engine heat softening the rubber hose) at that segment of hose line and restricting (or fully cutting off) gas flow thru the hose there
After reinstalling your cleaned or rebuilt and serviced carbs to your engine, did you synchronize the carbs to the engine and then also do the final setting of the "pilot mixture" screws of the carbs (1 pilot screw on each carb) ?
The synchro procedure ensures that each cylinder's combustion chamber is getting the air-fuel mix it needs from its carb - involves "matching" the throttle plates' openings to their respective cylinder's vacuum suck so that each cylinder is getting the proper air/fuel mix it needs. This is important too, especially when (as is often the case) the cylinders have mis-matched compression pressures (due to age and use and piston ring(s) wear and valve port(s) cleanliness and wear) - you are effectively matching that cylinder's mixture need to how open or closed the throttle plate in the carb feeding it is.
Several of us (if not many of us) have experienced similar issue(s) as you are now.
I myself read several times the VB Carb rebuild guide that
Long
Distance
Rider authored and posted permanently for us in this Carb and Fuel section of the forum before and during my carb dismantlings and rebuild and re-installation.
I made my own synchro device with 2 clear-glass bottles, some pink ATF (auto trans fluid) some skinny clear hose pieces and rubber "bottle caps" I could drill thru and insert (with a tight fit) the skinny hose pieces (I brought 1 bottle with me into my local Home Depot and bought a 4-pack of rubber furniture leg "non-skid" caps that slid-fit tightly onto my 2 bottles), a pair of Motion-Pro adapters (brass, $8.xx on eBay) for the skinny hose connections of my homemade device at the engine cylinders top (install into holes plugged by Honda with a small bolt - 1 on each cylinder - each bolt with what appeared to be fiber, not metal, flat washers, watched someone's YouTube video on the synchro procedure a few times, and was successful in getting my Twins to run correctly
AND before I did all that, I too was experiencing only one cylinder firing, like someone above mentioned may be happening with yours right now.
Glad yours is running, you'll get it running better and tuned properly sooner than you think, like I did. 
