On the MTX cars (you), there's a grommet really high on the firewall; under the wiper cowl. Or just drill a hole in the fire wall beside the clutch cable grommet. We automatic guys have that same grommet; but it's empty because of no clutch cable. So ATX guys; just use that.
As far as your amp being larger than, say, mine, the wall I built is mostly empty space. Meaning I could cut the amp hole a lot bigger and fit a larger amp in its place. I've also got a CD changer in there, too. How many and what size speakers do you have?