I am surprised none of the filters you tried solved the problem.
My guess is that the circuit design mistakenly includes a floating high impedance node.
Eh, high impedance maybe; just as likely, induced current in loops between the boards, or voltage drop between them -- for example, two boards joined by a cable have a dumbbell dipole antenna response, with the RF current flowing through only the low-impedance wires in the cable -- VCC/GND usually -- and thus incurring some voltage drop there,
and no voltage drop on the signal lines, thus CMRR is poor and noise corrupts the communication interface.
It could still be both, for example if they use I2C between boards. Almost certainly a terrible idea, but for a short cable to a small board, it can pass commercial levels. The catch being, I2C uses a couple kohm bus impedance (passive pull-up), so is relatively more sensitive to ambient E-field than most other interfaces (compare CMOS pin drivers in the <100 ohm range).
Ignition basically means steady-state repetitive EFT.
I2C does have the advantage, that it should ignore transients of some ns (officially, up to 50ns); but EFT could still be strong enough, or the subsequent ringing long enough in duration, to stretch beyond that time frame, and corrupt it.
There is still the problem of how it got there; 3ft is a respectable distance, compared to the likely length of spark plug cable, victim cable, etc. There's a lot of metal on an engine, and it's likely there are grounding metal cowlings around the ignition circuit, alternator, or anything else wired to it. (Why would ignition even be anywhere near the alternator?) Perhaps there are more plastic housings, or the metal parts are poorly connected (e.g. screws through painted parts, little or no connectivity), no idea.
We are talking pretty ridiculous source levels (10s kV), but depending on the route, we can't throw away too much of that before losing impact. For example, the cable might have some low 10s of dB CMRR, at relevant frequencies; a transient of 10s of V, maybe 100s even, applied directly to the board -- "direct" in the sense of relative proximity, say we put the two boards in a TEM cell -- might be required to corrupt it.
That leaves the conducted route as a strong contender, but conducted is also relatively easy to filter. The catch is, if neither unit has a meaningful ground / reference plane with which to filter against, it simply won't do anything; it can't be just shoved inline, it must be wired and placed properly.
Tim