What is the EGT gauge doing while the fuel flow is fluctuating? If it is doing nothing then it is probably the fuel flow gauge.
Further, what altitude are you at when it happens? The engines on both the C404 and 402 are prone to fuel flow problems at altitude - again the fix is to have the pumps on.
Lastly there was a modification for the pumps which required them to be on at all times to cure such fluctuations. Check whether your aircraft has been fitted with them. Incidentally, sometimes not even your engineers will know this so you need to check the flight manual for the amendment pages.
Before you flame me for this I was flying a C402 a few years ago and was idly leafing through the manual when I came across the relevant pages. When I mentioned it to the chief engineer he expressed some surprise at the fact. In his defence he hadn't carried out the modification.