I'm really not too sure about the vaccuum theory, as the area between the inner wheel well and fender is pretty well enclosed and therefore protected from that, especially on a vehicle that will most likely never see over 120 M.P.H. due to ECU speed limiting. Not to mention that the stock location has suited isuzu just fine over the years. Now, if you're talking about placing a scoop IN the inner fender well, and exposing the scoop to tire debris, water, etc. and air patterns, I would say DON'T.

Through-the-fender and on the outside of the fender might be a good airflow spot, if ducted to a stock type box for separating water and debris from air.

Another option might be to consider some kind of under-the-bumper scoop setup, like on the 1968 Olds 442. But that would hurt on the off-road side for general clearance and water-crossing abilities.

The custom airbox on my current VX is just the stock location, boxed-in with sheet aluminum at the rear and engine bay sides and a K&N cone filter.

If Joe Black fabs a hood, I'd like to see something like a cowl induction or forward facing scoop, the full width of the insert, with a 1/2" to 3/4" wall that raises the scoop entrance off the hoodline (that would take care of some water/debris problems by keeping the scoop up high) .

I'd suggest you try some photoshop or .pnt work before cutting holes in your fenders. Also buy replacements for the parts you cut if you ever decide to put it back to factory.