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I have a Long EZ with a Lycoming O-320 E2D. It had a complete top-end overhaul two years ago, in June 2017. All four cylinders were relined, and pistons and rings were replaced. Since then the aircraft has been hangered, in Oregon for one year, and then in Arizona (very dry). Since the top end overhaul the engine has had only 25 hours, and still has break-in oil in it. (one oil change six months ago).
The aircraft had thirty year old avionics, including a unreliable EGT/CHT gauge connected to only one cylinder. Recently I installed a new Dynon HDX Flat screen system with a full Engine Instrumentation (EMS) system that monitors and displays CHTs and EGTs on all four cylinders.

The problem is that now I can see the CHTs on all four cylinders, and they are much higher than I think they should be, even on the ground at idle. Lycoming documentation says absolute maximum CHT is 500F and maximum for continuous operation is 450F.
The first time I noticed it (two weeks ago), I had been taxiing or sitting waiting to take off for 20-30 minutes, and the CHTs on cylinders 3 & 4 were over 450F. (440F and 463F).

I took it to the local FBO and had them check it out. They did a compression check (all four cylinders were over 77/80), and bore-scoped the cylinders (all four were pristine, the A&P said that the cylinder walls appeared to not even be broken in yet). The only recommendation was that the engine baffling was in very poor shape.

So I completely rebuilt all the engine baffling. But this did not fix the problem. Even on the ground, taxiing out to the runway, CHTs on 3&4 climbed to over 400F, although they did not get to 450F. I did a Test flight, and in the climb-out (90-100kt, 2480rpm) CHTs would climb to 430F. Once I reached altitude and leveled off and accelerated to 130Kt, the CHTs settled back down to mid 300s. Another strange thing is that the cylinders that are reading high are inconsistent. On the ground, it is 3 & 4 that read higher. During climb-out in flight, cylinders 2 & 3 are the high ones. This sounds to me like an airflow issue, like the baffling is not right.

So this is my question, Given that compression checks are good, indicating valves are ok, and the cylinder walls are clean indicating no top end corrosion since the overhaul, what else can cause high CHTs? I have been told that engines run hotter than normal during break-in, but is this factor alone sufficient to explain these readings? What else should I be checking? I don't want to be relying on an engine that has a fundamental issue that might cause it to seize up on me.

Thanks in advance!

Your temperatures don't sound all that bad for breaking in cylinders, but you should go back over the baffling. The baffling is there to maintain pressure in the plenum with the help of those rubber strip seals, and to force air at high velocity between the cylinder fins as it makes its way through to the low pressure side. The baffling has to be right against the fins so air can't go around the fins. Baffles that don't fit properly prevents the air from picking up enough heat from the fins and even if you have normal temps you can have hot spots.

Yes cylinders will run hot as the piston rings wear off the ridges of the honed surface of the cylinder wall. On the other hand, I wouldn't be surprised at all to see high cylinder temps after 20 minutes of ground running on any tightly cowled pusher where the airflow is only from a gentle suction on the exhaust side from the prop. If you're at idle and the wind is behind you opposing what little cooling flow there is, typical when sitting in a line up on a taxi way, the engine is getting very little cooling flow at all so naturally you have an Easy Bake Oven running behind you.

In a Long Eze you should avoid long idle periods like that, especially during break-in. Especially out of wind. And in fact, until break-in is complete (oil consumption will stabilize and CHTs will drop) you should avoid flying in circumstances where you have to sit in line on a taxiway without shutting down (At Oshkosh I remember watching the Eze drivers shut down, get out and push their planes along as the departure line of aircraft moved along to avoid the 20 minute ground run cooking their engines during the post airshow escape crush).

Another minor point is, if the EGTs are working off thermocouple washers instead of the screw-in probes of the threaded hole provided for the purpose under the Lycoming cylinder, the CHTs will read higher because the area around the plug where the washer senses gets the heat from the plug, which is always hotter than the surrounding aluminum. Especially if they are washers on the lower plugs (Continentals use the washers, usually on the top plugs - Lycomings have the dedicated temperature probe well underneath, but sometimes you will find the washers used on Lycs if it was a later add on).