Is my engine running lean?

From your description regarding the issue is also related to weather temp. Check the spark plugs gaps. 

I have tried both the max and min gaps and no apparent change..

Your original post doesn’t make it clear to me but some things that passed through my mind follow.  So does the engine pass or fail the 4,000 rpm ignition circuit check with regards to rpm drop, and rpm difference between circuits? What are those numbers? Under what situations does the rough running begin to appear? What makes it worse, or makes it better? Does the engine run smoothly on both ignition circuits at idle? What about at idle, on an individual ignition circuit- how many rpm do you lose on each circuit and how does the engine run? Repeat with the crossover air tube clamped closed, does this roughness increase, decrease, remain the same, or smooth out at idle? And at 4,000 rpm? You balanced the carbs but confirm the idle speed screw on each side is set to how many turns out from fully seated? Cold start system confirmed fully closed at each carburetor when the Bowden cable in the cockpit is pushed to closed position? What are your engine compression numbers for cylinders 3 and 4 as compared to 1 and 2? Have you dynamically balanced the propeller to the engine and not changed pitch since doing so?  By the by, I suspect I know exactly who you bought that engine from but that’s my story for another time as well.  

So I pulled the carbs and went through them top to bottom.. no surprises for an engine with 80 hrs.. verified everything was correct .. needle clip in position 3, 158 main jet 2.72 needle jet 1.5 turns on idle jet. blew everything out and all passages were good. put back together balanced carbs.. Today is relatively warm sunny day so it ran great with acceptable mag drops although too windy to fly. I will run it again as soon as the weather cooperates and report back. Probably ran engine for almost 30 min and no change to color of plugs FYI.. 

Some things I tried while I was there as per Jim .. I did clamp crossover and no difference on mag drops.. pass or fail seems do depend on how cold it is outside. when warm pass right mag drop is 100-200rpm and left mag is 250-300. When cold it was right 100-200 and left 350-425 .. Engine does feel pretty smooth with both ingnitions on. At idle it seems like roughly the same drop or funny enough a bit larger drop on right mag.. rough running was appearing mostly in straight and level flight .. climb was smooth then when I would level out and speed would increase roughness would develop.  Oh and yes the chokes are properly closing.. 

a bit of food for thought on the prop and balancing.. I was running a powerfin ground adjustable and decided I wanted to try something different as well as to see if it would help. I purchased an In-flight IVO prop and as far as I am concerned it is an awesome addition for the money. but relevance to this I can now pitch in flight so I pitch for a short takeoff then drop it down in the air. It seems to help when I notice any vibration to pitch it a bit coarser and pull the engine down a hundred rpm (no I am not lugging the engine. course for me is still 5600 WOT). but I have not balanced it dynamically as I don't have access to a balancer and have not called around. The issue has been there with both propellers though and it really doesn't answer my original question as to why the rear cylinders are burning the plugs white while the front are black.I have not checked compression but I do have a leakdown tester that I will hook up next time I am there..

Sorry for the long winded response..

Hmm, engine begins to run rough as you accelerate? Float bowl vent tubes tucked up tight inside the cowl where they should be? Engine fuel pump vent line tucked inside the cowl? As far as the colder it gets, the roughness appears, that’s a puzzler.  Left side fails when cold.  So either false air is entering the cylinder, leaning the mixture but not enough to make a difference when temps are warm, but when cold, the denser air requires more fuel but the carb does not “know” about the false air and therefore does not compensate by enriching the mixture; or the cold temperatures are inducing an ignition failure somewhere.  When it is cold out and the left side fails the run up check, does swapping the circuit leads move the problem to the right?