Can't they check a list of all parts and components? If the Pentagon doesn't have such lists, I'm sure Russia or China can get them one. 
Nope. Put your tinfoil hat on, but all those instruments put out electromagnetic fields. Those fields may combine or fall out, like any wave forms to provide areas inside the cockpit with high or low EM concentrations, and those concentrations at specific frequencies may have an effect on perception or cognition.
After all, the brain is an electrochemical computer.
If those fields/frequencies are detracting from pilot performance, or combining to do so, then some sort of adjustment must be made or shielding installed for the pilot to have optimal performance.
The very devices that are there to make the pilot more capable may be rendering him/her less so.
I would think that someone, somewhere, has studied at least some of the effects of EM radiation on brain function, maybe DARPA, maybe as part of MK-ULTRA or some other program. If so, it is a question of putting that information with a 3-D map of the EM field strengths/frequencies in the cockpit to figure out what is interfering with performance, and those frequencies/fields may be subject to change depending on what armaments or features are being utilized.
Once that is done and the assessment of the effects made, countermeasures can be taken to prevent performance degradation.