Triumph Bonneville America 2002, misfires for first 10 miles or so, then suddenly clears and runs well. Appears to be running on one cylinder.

carbs need adjusting for vacuum alignment replace the spark plug on that side and make sure the wire doesn't begin to short out when hot?

First need to use the right spark plug-for you motorcycle need to be
Champion-N 3 or equivalent.
Valve timing - Inlet opens-0-190 ins.(4.85mm ) at T.D.C
Exhaust closes-0.130 ins.(3.27mm ) at T.D.C.
After this check you need to clear and adjustment carburetor.

Straight from the website Bonneville America Manual

Put a test light on the coil packs see if they're giving you Sparks

To start with, your battery was probably already low. You have to be at about 4000 rpm for the charging system to kick in and put out 14v or so. So if you just sit and idle, you will eventually run the battery down. If it is already low, you may have run it down below where there are enough amps to start it again. I know my 2002 BA started having what appears to be charging or regulating problems and the batteries won't stay charged. Try charging the battery with a good trickle charger to begin with. Then, when it is fully charged, run the bike and see if the charging system is keeping things up.
Mike

Just a very quick check,Swap the sparkplugs over.Don't put in new ones.If the problem follows that plug,it is only the sparkplug.Hope you get it fixed