Strange misfire issue on 15 SE...

So to start things off I got this car for free from a friend. Engine overheated badly and head gasket blew and then sat with water in cylinders ruining it. I got a replacement engine where I was scammed that also had water in cylinders and rust but was savable. (had to use crank from old motor as the ""new"" motor had the harmonic balancer bolt sheared off in the crankshaft so that was just unusable. I replaced con rod bearings, and all piston rings. However I reused the crank bearings as the engine still spun freely when everything was torqued to spec. Among other things replaced were front main seal, rear main seal, water pump, head gasket, head bolts.) After rebuilding the engine and putting it in my fiesta it honestly runs great... except for if you hold it in S in 1st gear (or any gear really) above 4k rpm for more than about 5 seconds. The CEL starts flashing and shows codes for misfiring on cylinders 2 and 3. The misfire quickly goes away after you bring the rpm down and if you just let it go through the gears, it never flashes the cel. Its only when going full beans onto the highway, or driving on the highway when its hot as hell outside, where it will randomly start misfiring on 2 and 3. Now I will add the radiator is not working very well at all and the car is running rather warm (no bubbling in overflow res, no coolant in oil or oil in coolant, and the color changing head gasket tester stuff showed that it was fine) as my code scanner reports it runs at ~216 F with the AC on at 60mph. I will be replacing the radiator asap. So I'd like to know if this is just a temperature issue, or if perhaps I didn't reassemble something correctly, or quite what even is happening. More of note: no blow by from dip stick tube but there is a lot of, what just seems like air being blown out of the oil fill cap if you take it off while running, dunno if thats normal or not. Cylinders 1 and 4 never ever misfire either which is all the more weird.
I have tried some things to try and remedy this issue. Replaced spark plugs on all cylinders (gave noticeable low end pickup in power) replaced coil pack, swapped plug wires between spark plugs. I still need to plug forscan into the car to see exactly when and at what RPM its misfiring. I also still need to try swapping injectors and checking fuel pressure but i just doubt that being the issue. I also have yet to check compression but when turning over it sounds very even in just audible compression. Another thing I noticed is a weird round thing that has a plug going to it on the right side of the intake manifold that is rubber isolated and attached to a metal bracket and it will sometimes just start clicking like crazy. Is that normal? Sorry for all the questions this car has been a real head scratcher for a little while now.