Now that I have some time on my AeroVee, several lessons learned are worth mentioning. Hopefully, these comments will save other builders from some frustrations with their own engines. I'll try to put in all the "I wish I'd known that..." info, as well as the "Next time around I'll do it like this..." info.
AeroCarb Mixture Setup
Don't set up the AeroCarb too rich initially, even if the engine is running hot. Resist the temptation to richen the needle setting in an attempt to cool the engine. It won't provide much additional cooling, and will make the engine run very poorly. When it's running poorly, you run the risk of misdiagnosing problems and chasing a lot of dead ends. For example, slobbering rich, the engine will want to die on landing. It may hesitate at taking power (like on a go-around), or surge coming down final. All of these things happened to me. Once I leaned the mixture out properly, these symptoms went away. I recently verified this by richening my mixture about 1/8 turn. Once again, the engine ran hot, and very poorly, on the ground and in the air. If you have cooling problems, don't try to solve them by running rich! (I can't emphasize this enough)
Don't be afraid to pull the mixture knob to get the engine running smoothly. My mixture is set up slightly rich at all throttle settings. I simply pull the mixture knob out a bit to get the engine to run like I want it to. On taxi, the mixture is out 1". On take off, about 1/2". During cruise, I lean until I get about 1300 EGT, and that's about 3/4" on the mixture knob.
My engine runs rather rough when the mixture is rich. It really smoothes out and purrs at about 1275-1325 EGT's.
I you try to set the main needle mixture too lean, the engine gets really "finicky". It's much easier to be just a touch on the rich side and lean out with the mixture knob. This was very counter-intuitive for me, but seems to be the case.
The Fence Baffles really work well to bring down engine temperatures. However, make sure the baffles are well sealed. Pay particular attention to the edges of the baffles where they contact or sit next to the engine structure. The big gap by the starter makes it hard to get a tight fit, but find a way to seal it up. My experience shows that just sealing things up well is worth about 10-15 degrees alone.
Engine temperatures will climb rapidly when airspeed is low (e.g. during initial climbout). This is normal. If you're fighting high CHT's try climbing out at 90-100 instead of 70-80. The added cooling airflow will do wonders for controlling the CHT's.
Make sure you place the CHT senders between the spark plug and the plug washer, not directly against the head. At best, this makes comparing your temps to the factory temps difficult (as this is how they measure CHT), and at worst may be casuing leaking at the plugs.
Adjust the carb slide so that at full throttle, the slide is "ever-so-slightly" closed (approximately 1/16"-1/8"). This will prevent engine stumbling and rough operation at full throttle. To check this, fly level at full throttle for a few moments to let the engine rpm and airspeed stabilize. pull the throttle back just a "smidge"...if you have a vernier throttle, try 1 turn out. If the rpm goes up (20-80 rpm), the throttle position needs to be adjusted.
Make certain the throttle operates freely and doesn't stick at all. Sonex published a service bulletin about slightly chamfering the slide corners to prevent binding. This modification is worth doing, or at least opening up the AeroCarb to have a look at it. Also, while you're at it, make sure there are no burs or machining debris inside the AeroCarb. Lastly, make sure the throttle cable is well supported on it's way to the throttle arm. The cable should be straight into the carb for the last 6 inches or so. The built-in throttle cable clamp is not enough to ensure smooth movement of the slide.
General Engine Setup
Double check the socket head screws that hold the magnet cover in place on the flywheel. If they are loose and/or don't have locktight, the cover may shift position and strike the magnatrons, ruining the magnet and possibly the magnatrons themselves.
Time the secondary (electronic) ignition using an inductive timing light. In the end, it'll probably save you a bunch of time, hassle and headaches.