You cannot have any leaks at the exhaust headers at the heads or it will totally mess up the A/F ratio as seen by the O2 sensor. Plus as other stated - you must run an exhaust connected to the header - otherwise it also screws up the O2 sensor. Suggest start here.
I'm also not sure what you mean that the port on the front of the intake is plugged? Does that mean you don't have a PCV valve installed? I've attached a photo of the stock PCV valve
You did the right thing by adding a filter onto the port by the oil filler cap. That allows clean air to flow into the crankcase - assuming that you have a PCV valve installed.
If your FP gauge pegs at >60 psi, something is wrong. If the pressure is 58-60, then that should be fine. I've attached a photo of the correct hookup for the filter/regulator return to the tank. Suggest double check that the 5/16" fitting in the center of the regulator goes back to the tank unobstructed/unrestricted.
My system is FAST, so I probably cant help you with the setup of your Megasquirt system.
Keep us posted on progress.
Jim
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