testing single changes is good to see what makes a difference, but it also doesn’t assume there’s exactly one issue going on either, so you might need more than one fix.
a pretty common theme on commercial stuff is to have small caps (like 1-10nF) to ground on used inputs/outputs etc, keeps interference from entering and leaving the board.
if there’s a lot of emi you might need to put a small inductor or resistor in series to reduce the currents carrying the emi in or out from the board.
let’s say there is emi generated on the board with spectral content on 144MHz. this will conduct to every wire leaving the board.
conducted emi can be pretty hard to deal with, sometimes requiring a shielded box and nothing can enter/exit without having one of the above mentioned filters on it.