Need more info. What model of O-540 is it? Is the carburetor on the bottom or the back of the engine? The O-540-J3C5D and -L3C5D engines use an intake manifold, cast into the oil sump, that looks like this:
View attachment 132106
Viewed from the right rear. The HA-6 carb bolts onto those four studs on the back. The air/fuel mixture goes horizontally into that duct running forward, where the mixture hits a wall and goes left and right into the six induction tubes. The numbers on those tubes are parts catalog reference numbers, not cylinder numbers. The cylinders are numbered 1-3-5, from front to back, down the right (copilot's) side, the side nearest us in the picture. 2-4-6 run down the left side. So your #3 is the middle one on the right, and it runs cool. The #4 is the middle one on the left, and it runs hot. Now you'll see that the #3 is taken from the bottom of the manifold, while #4 comes off the top.
That air/fuel mixture, in striking the wall, leaves some fuel on it that runs down and gets into the bottom tubes, #3 and #6. They run rich, and therefore cool. The top ones, #4 and #5, come off the top and are leaner and so hotter.
It's unfortunate. We had a factory-overhauled J3C5D (in an R182) that had a real problem with this. Those two bottom-fed cylinders would actually flood and quit at idle. The carb was brand-new, and had a defective fuel nozzle in it that was not atomizing the fuel properly. Lyc sent me another carb that fixed the problem, along with an invoice for $8800.00 for the carb in case I didn't send the defective one back. You really don't want to have to buy one of those things. And that price was 15 years ago.