Hya there bro, DONT GIVE UP!! (REALLY),
For instance, my F2 was taken off the road nearly three years ago, for what should have been an engine rebuild, BUT, one thing led to another, shortage of funds happened, life happened, many things went wrong, and its still not finished ( but everything that is looks stunning!!)......AND it will be finished for next summer, whatever happens!!
Anyways, one thought i had about yours,was this..........You burnt a valve in the old motor? yes? and you replaced the motor with another unit. I bet you used the carbs that were attached to your old motor?
in other words, a "new to you" motor went in , but you used the carbs off your old motor right?
RIght, if this is correct, then did you find the CAUSE of a "burnt valve"

Because one thing that will definately "burn a valve" is running to LEAN, and guess what? If your bike responds well to "Pulling on the choke" ( because when its warmed up it SHOULD NOT) then that would suggest it is "Still running lean" and the common denominator here is "The carb mounting rubbers" which if split or cracked and drawing in air,would cause it to "run lean"
Make your first port of call to take them off,examine them one at a time, (properly) and if they are split cracked or even old and hard, then change them for new ones, while you are at it, check that the retaining clips are doing their job, and tightening up properly.
If there is no joy here, go back to the carbs, and work your way through them AGAIN, I know, I know its a bind, but the evidence points to running lean. check float height,clean out the jets meticulousely. and remember, a set of carbs thats set up and balanced for one engine will not be set up and balanced for another engine, as NO two motors are the same.
good luck, and when it feels like you arent gonna get there, remember, YOU WILL!
All the help you need is right here!