"The engine is mounted as in the Ford Model A with the axis of the crankshaft horizontal, so the troughs in the oil tray all contain the same amount of oil."
The Model A engine was not mounted horizontally. It had a 3 degree tilt to the rear so oil could flow back and excess oil flowed into the overflow pipe that directed oil to the front of the dipper trey for the rods.
As I think about this more, I think that mounting the engine horizontially so that all chambers received the "same amount of oil" was a mistake. You will note that the dams in the valve chamber are of different heights to control the oil levels. All that is needed is to oil to the main bearings and camshaft tubes, which are not very high, plus some splash to cool the valve stems. All else goes to the dipper trey. Mount the engine so there is a slope to the rear so excess oil goes to the dipper trey.
All excess oil, and there must be excess oil, must flow to the overflow tube into the dipper trey and this is mandatory. The #4 piston would be the last to receive any overflow, if any, and that probably explains why # 4 blew. My guess is insufficient oil to #4 because the horizontal mounted engine did not flow sufficient oil to the dipper trey. Once oil is in the dipper trey it must flow to the rear, ie, to #4, which a horizontal engine or dipper trey will not do.
If you are going to run over 3000 rpm regularly, I suggest you open up the dippers per the attached (I hope) photos. I actually open them a bit more than shown in the photos, which were a test. Its easy with a dremel tool.
I also suggest you open up the oil pump to flow more oil if you are over 3000 regularly. This involves turning down the shaft and opening up the the inlets and the outlets. There is a website on this and I am sorry I cannot find it right now. More oil flow will get more oil to the valve chamber and overflows to the dipper trey to the rods if the engine is sloped to the rear. This must be done to protect #4. The overflow from the valve chamber is the only source of oil to the dipper trey.
My conclusion is that your engine failed because of insufficient piston clearance (.002 is not enough as stated above) and insufficient oil flow to the dipper trey because of the horizontal engine. If properly set up, 3000 should not be a problem, but I would not run a stock set up engine at that speed very long. As your test shows, about 10 minutes is max.
Take care of these things and see how coolant and ignition timing work out. Coolant and timing are not your primary problem, although it is nice to think so because they are easy to deal with. Oil and clearances are the problems and that is going to take some work but you are going to feel good when you get it right. I do like the car, and putting an A in it intrigues me. Good Luck and Best Wishes.