Most of the time it would pop and miss out, in any gear, when less than 3000 rpm.
Are you describing an "igntion" issue or a "transmission" issue when you say "pop and miss out"? I hope you're referring to a spark event given the reference earlier to timing marks.
If you removed the igntion plate, and the points cam, it is possible you installed the point cam 180* out. There's a very faint dimple on the circumference that aligns to a spot on the ignition plate. This can cause problems aligning the timing marks.
With your 836 kit, did you use a stock camshaft or aftermarket? Did you degree in the cam? Do you have an adjustable cam sprocket, or is everything other than the overbore fully stock?
Avoid shifting the bike under 3,000 RPMs too. Thats lugging the engine and your SOHC doesn't prefer that rev range. Crank it up above 6,000 and run it nearer to 9,000. Your motor will thank you, and your grin will increase like it was fueled by Viagra