Jbosma, When I installed the 4 into 1 exhaust on my bike I jetted up 1 size on both pilots & mains. It ran rich and I had a hard time tuning with an inconsistent idle and hot stalling occasionally at stop lights. I noticed that #3 was @80F colder than the other 3 cylinders and I could not "tune it out". After trying everything I swapped the guts (all brass parts) from #3 to #4 and the problem moved to #4. This was a start but with all new jets I was confused but on the right track. Pulled carbs again and jets found that the after market pilots had burs in the jet passage causing restriction and a messed up flow pattern that I confirmed by spraying carb spray thru them. My fix was to clean & reinstall the stock jets (pilots & mains) and the bike runs great. With the stock airbox & filter I did not need to upjet for the pipe.
I am sharing this story because you may have a pilot circuit partially obstructed causing the cold cyl. If you have already swapped spark plugs and still have the cold cyl then I would look at pulling the carbs, giving them a clean and verify all the pilot & main circuits are clear.