We need some pictures as I can't visualise what the problems are.
I made a crossmember to mount the intercooler and standard 8v radiator on my conversion, also using solid engine mounts meant I could delete the snub mount and fit a toyosport intercooler higher up to clear the bumper. The S2 intercooler setup puts the inlet and outlet on the left side so you need to find space for the pipework to go across to the right side.