On the more random misfire some thing that has popped into my nogin was the old sticky valve syndrome you used to get on the old zetec engines, where although the valve goes up and down it doesn't rotate in the seat as normal due to the incorrect oil viscosity which caused them to stick open causing a misfire as it gets hot on one side, i cant remember if he fl2 is bucket and shim or hydralic tappets but a dodgy shim or bucket could be the cause of the issues
You may be on to something there. When I was putting the engine back together, I noticed one of the rockers on No3 cylinder (inlet I think it was) was loose, as in it wasn't being loaded by the hydraulic adjuster. I assumed it would improve as the hydraulic adjuster filled with oil after starting. I also noticed that the valves in this engine don't rotate as the engine runs. This to me is unusual, as I'm used to engines where the valves spin by action of the opening cycle. This design isn't like that, and the valve stems have U shape wear patterns on the top as a result.
Then the engine is started from cold, it definitely runs on 3 cylinders, and the exhaust makes a distinct chuff on the non running cylinder, so it could well be down to an exhaust valve not seating until it's warmed up. However this starting on 3 soon rectifies itself, and once it's running on 4 constantly, it's smooth as silk, unless I give it decent throttle above 2500 RPM.