[craigh]

I had the same problem with a standard 3 inch air filter touching the bonnet,so i changed it to a 2 inch and it now clears ok,you can purchase a deep dish filter which sits further down on the carb to allow under bonnet clearence
when i fitted my body it was placed directly on the neoprene sponge on the transmission tunnel and allowed to settle,i found that some of the mounting holes needed elongating slightly to get them to line up,but managed to fit all of them.The suspension was then raised to get the correct clearence for the wheels via the adjustment on the coilovers:tu