IR laser readings on those headers will probably be inaccurate and will definitely vary depending on where you're taking the temp. Emissivity impacts the accuracy of your reading, and shiny/reflective objects are the most difficult to get an accurate reading on. So on your headers, cylinder 2 and 4 may give pretty different readings due to the color differences, even if the temp is the same.
I guess my point is, don't take the readings as accurate. You can, however, use them to compare one tube to the next (assuming similar color/sheen) or compare each cylinder to itself while doing some tuning.