Several things occur:-
the timing at both 3,000 rpm
What's the significance of this figure? That's the full-advance rpm for points, not Boyer
-Bransden e.i., which are fully-advanced at around 5,000 rpm; however, when checking full-advance, you have to check that your individual ignition does stop advancing at that figure.
Are 5 KOhm resistor plugs or caps fitted? B-B red box has digital electronics and requires one or the other.
Which alternator rotor mark are you using to time? The rotor should have six lines, three marked "A" and three marked "B"; most triples use the "B" marks but early ones use the "A" - different crankshaft keyway position. So, especially as yours is a '69, you should check with the crankshaft timing mark (under large hex. head on the front of the timing-side crankcase) and plug.
I've had the carbs cleaned twice,
checked that the idle passages - all the way from the air filter and float bowl to the little holes in the main choke either side of the engine side of each slide - are clear? Fwiw, the tickover sounded a little high on your video, my triples tick over at around 750 rpm when warm.
if anyone has any tips on how to properly start these bikes
Mike's are good, except I hold the throttle just a little open, not half.
The stutter could be a plug, they foul easy on this model at the lower revs, If using B8ES try a no 7 hotter plug.
Mmmm ... I prefer to stick with the recommended heat - Champion N3, NGK B8 - but use a plug that works over a wider range. I started using B8EV (thin unobtanium/costalotium alloy electrode) back in the late 1970's, now use B8EVX, I get at least the 10,000 miles per set that the manuals
say, I also consistently get 2-3 mpg more.
As your bike's e.i. requires resistor plugs, imho try NGK BR8EIX.
I'll double check the voltage on the battery and get it hooked up to a tender.
. Would I be correct in thinking the bike has three 6V coils? My experience and humble opinion of 6V coils on a triple
. If you must use 6V coils, bear in mind that the e.i. is nominally 12V so, because of the electronics, the battery should produce at least 13V, any less and the coils get less and produce an even-worse spark.
. You should check that the battery is maintaining Volts under load - just checking it without any load isn't any good.
. You should check that all battery Volts are arriving at the e.i. 'box' - i.e. there isn't any Voltage drop between battery and 'box'.
. While you're checking electrics, how is the return to battery positive (assuming standard electrics, not 'converted to negative ground') made? Because Boyer
-Bransden fitting instructions don't specifically recommend otherwise, fitters are apt to connect the 'box' Red cable and last coil +ve to whatever. Ime and mho, this is A Bad Idea; those connections should be extended in dedicated cables to battery +ve specifically.
. I would exercise care with a battery tender, there are too many stories for too long that they eventually do the battery they're supposed to be 'tending'. I've only ever used a normal battery charger - albeit one capable of delivering the small Ah necessary to charge a motorcycle battery correctly - charging any unused battery about once a month and I feel cheated if I don't get at least a decade out of even a conventional lead/acid battery.