First, hot EGT's are not indicative of anything. Hot relative to peak is. EGT readings are very dependent upon many things, including where the probe is situated, RPM, Throttle position, and lastly, mixture. Comparing raw EGT temperatures from side to side is not a real good test for these reasons, unless everything is exactly the same...and it never is!
Fuel flow- the only way to get the fuel flows exactly matched is to send both servos out and have them bench flow checked and matched. Otherwise you are limited to adjusting the idle mixture for below 1100 rpm fuel flows, but that will have some effect on the higher end, but not much. Specs for the IO-320 engine are takeoff FF of 13.6-16.8 GPH at full power, sea level, std day according to Lyc. That is the spec, you can choose to have the engine set up anywhere in the spec.
CHT- BAFFLES, BAFFLES, BAFFLES!!!!!!! Ok, lets start with the flexible baffle on the nose bowl, that should be visible in the inlet. It should run from under the lip of the nose bowl, and should be OVER the top of the front cyl baffle. If it is under the lip, all the high pressure air is going to the lower deck, and decreasing cooling efficiency significantly. Next, look at the baffle material along the cyl. It should be on the pressure side (inside) of the hard baffle if it is attached by rivits. If it is on the outside, and in good shape, use copious amounts of RTV on the inside where the soft baffle meets the hard baffle, so no air escapes through the gaps. Next, look at the soft baffle on the rear baffle. It should be compressed and pointed forward so the pressure makes the seal tighter, not allowing air to shelf over the baffle. Fill any holes, and all areas between the baffle and the case with RTV to maximise the efficiency. Think like the air coming in the front. Try to maximise the pressure on top of the engine (uper deck) and minimise the pressure below the engine (lower deck) and the greater the delta P, the more efficient the cooling will be.
-Zach