Look your Filter Minder over carefully for cracks. Mine cracked and would indicate wrong. I bought a replacement and all was well.
FWIW, I used a vacuum pump to check the calibration of the new one to Fleetguard air pressure drop specs for used up air filter and it was right on.
So IMHO, they're well worth using.
As far as modifying the air box, if you are indeed over-powering the filter (with eng mods) then that can really help. Many operators have used what is commonly referred to as the Home Depot intake which is a 3 or 4 inch hole and a pipe connected that sucks in fresh air. The filter minder doesn't pull down afterwards.
Those that always bash any kind of eng mods will certainly have something to say about this kind of thing but those in the know will tell you otherwise and I've seen dyno runs that prove it.