To me, the most disturbing thing about the plugs is that they aren't all the same condition.
There is clearly something dissimilar with # 3 that you will have to discover, even though it's looking like the best running cylinder. I'd probably scrutinize the slow jet in the carb of #3. See if the orifice is clear and supplying the same amount of fuel as in the other carbs. When they all behave the same, you can then make identical adjustments to all in order to bring the combustion conditions into a reliable state.
What is the carb set up number stamped on the carbs? 022A?
What settings did you chose for your carbs?
Are there Honda parts in the carbs? Slide needles? Emulsion tubes?
Are the float heights the same?
Are the idle air bleed screws settings the same and where are they set?
Does no. 3 intake runner have an air leak?
Are your air filters over oiled except for number 3?
You can expect cyls 1,2, & 4 to shortly stop working as the carbon on the ceramic insulator will soon be an easier path for the spark than the gap.
Right now, though, you could rotate the other plugs through #3 cyl. to clean them off!
If you don't have a sand blaster to clean the insulator soot, I just recently tried PJ's tip for cleaning with a propane torch. It worked pretty well, even though a bit worrisome seeing glowing red electrodes. Recheck/adjust the gap afterwards.
Otherwise, plan on getting another set of plugs to recover from dead cylinders.
Did you ever do a compression check to see if the compression is even across the bank?
You didn't really think you were done working on the bike did you?
We have an adage in the engineering community. "The last 10% of the project takes 90% of the time."
You may think you just changed parts on the bike. The ones that weren't purely cosmetic need re-engineering. And, the adage applies.
How far away is your test track?
I hope you consider knowledge as part of the end result of the project. I personally, believe that is more valuable an asset than the finished bike. But, I suppose some will disagree.
Cheers,