hey, not really sure what u mean about cutting the brackets to install the nuts?
i have some pics here that may help.
This is how i cut my front bumper rebar to fit around the intercooler (maintains bumper support under headlights to prevents "sagging bumper syndrome)
I do know when i mounted the rebar/brackets back into the frame rails i had them bolted to the rebar/bumper support still (brackets slide into the frame rails and there is two bolts that come up from the bottom of the frame rails to securre them. In the pics you show it looks like you removed the bumper rebar/support from the brackets. That should solve your problem. The intercooler itself mounts to two pre-drilled and tapped holes in the rad support and there should be two clearish poly bushings to go inbetween the intercooler and the rad support. Bolt the intercooler up, connect all the piping/couplers... then slide the cut and modified bumper rebar/support and brackets into the frame rails and secure with the 4 bolts that come up from the bottom of the rails (there are holes underneath cut in the rails from factory to access these bolts.)
hope that helps
oh also, i removed the power steering cooler loop out of there to make room for the FMIC. i just cut one of the PS return hoses a little shorter and routed it back to the resivour totally removing the cooler. never had a issue in daily driving it without that PS cooler loop pipe.
also your car being automatic appears to have a cooler mounted on the drivers side for the tranny oil. Hopfully that doesn't interfere with the intercooler/piping routing as well or you may have to re-postition the trans oil cooler as well.