So I am trying to break in my freshly rebuilt 312. I have fired it off twice now, but have shut it down early due to the #1 & #3 cylinders getting hotter than the others. The #2 & #4 are not getting hot at all. #5,#6, #7 & #8 on other side seem pretty evenly distributed. The exhaust header is glowing red within a minute on 1 & 3. I assumed a vacuum leak after the first time. I replaced the intake gaskets and checked for flatness etc. while doing it. I am running a 3x2 edelbrock with Stromberg 97's. I have the front and back blocked off for this break-in so I am pretty confident that there is no vacuum leak there. After replacing the gaskets there wasn't any change other than the #4 cylinder seemed to liven up. #1 & #3 still hot and #2 not. Just to clarify when I say "hot", I am using an IR thermometer pointing at the header pipe 3-4 inches out of the head. I am getting avg. 300 deg on LH Side and 450-500+ on the #1 and especially the #3. This is with just a couple minutes of running at 2K rpm. I am afraid that I'm not doing the cam any favors by not running it in properly, but at the same time I don't want to cause more problems by running it in for 20+ minutes like it is. Any suggestions? 

I would be more concerned about no or very little temperature than cylinders that are running 150-200°F higher than some of the others at fast idle.  Possible causes for the higher heat signatures would include piston/cylinder clearances, piston ring gaps, cylinder hone crosshatch, unequal firing within the distributor, mud dauber buildups within header tubes, and valve lash.  You didn’t say what the cold temperatures were but these would require more scrutiny than the warmer cylinders right now.  Seeing as you’ve already got the engine turned off, recheck the valve lash settings for the cylinders in question.  Excessive valve lash can allow the cylinders to run hotter.  If the water temperature is staying normal, then give the individual cylinder IR readings some latitude.

Lorena, Texas (South of Waco)

Thanks for the advice! I will check the valve lash and go from there. The "cold" temps were in the 200's while the avg. was in the 300's. So maybe not much concern yet. Oil pressure and water temp were good, 65 psi & 160 Deg resp. As for the mud daubers, I built the stainless headers new, but it did take over a year before all of the nests in this old Model A body to finally reveal themselves! Lol Thanks Again!