Sounds to me like you have set the valves wrong to the timing - did you put everything back in the correct order and place it where it came from - pushrods back where they came from eg left exhaust to left exhaust etc if you have mixed things up it may cause problems, maybe the push rod have not been seated correctly or the barrel, heads or cams have not seated correctly when torqued down I would suggest you remove everything and re check your work and each component make sure you have not bent a pushrod or put anything back on in the wrong place. Then turn the engine over by hand slowly and watch that the whole sequence of tdc and valves opening closing is correct. This is not going to be a carb problem if you have not touched them - the flame front is burning in your exhaust making it glow. Did you check the condition of your valves and seats before re assembly.
Was the bike fine before you did the work ? have you altered anything else.
If not it seems simply that the exhaust valve is opening too soon or not closing properly for some reason.
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