If I were asked to look at it, one of the first things I'd do is verify analog voltages coming in. A volt meter can verify TPS, MAP, CTS, and other values AT THE ECU. Are there discrepancies between the observed values & the displayed values? If I know the analog signal is present, and at a proper voltage, next I'd check the ECU configurations.
Although I'm not familiar with the specific Holley unit, most Stand-Alone's allow you to configure inputs as digital or analog. If analog, you can scale the low/high thresholds (0-5, 0-15). I'd go back & review the CONFIGs in the software.
I would then break out the O-scope (which most people don't have) and watch digital signals like CPS, CMS, etc. It might be a glitchy digital signal indicating possibly a questionable ground or connector pin (mentioned many times already) or EMF interference from a coil or injector or something.
It is apparent your issues are not Standard Answer Number 1. You may need to just look at different things and let the system guide you to the issue. (I do electronics for a living and what might jump out at me as obvious may be missed by someone not as familiar with electronics.). Hope this helps.
