use a high speed steel cutter. i have a 1/4 inch bit and a 5/16 inch bit. they work very well on aluminum. dont use a tungsten carbide bit. it makes extremely tiny little splinters and if they get in your skin they dont come out for up to 5 weeks. trust me, i know.[:@]

as to where to remove material, some pics of the buggy with its components on the chassis and the chassis plat itself would be very helpful.