I would say if you got a quality file, and kept it clean while working, you could do it that way. Also a dremel tool with a quality bit in it could work as well. I 'may' have to hammer my strut tower a bit, but its got almost an inch clearance, and my motor shouldnt be moving that much.
As for the turbo, I will be getting like a 100* bent aluminum tube to weld to the compressor outlet. I thought about the silicone like J. has, but I think it would end up melting that close to the exhaust manifold. Ill also be making some sort of heat shield to over the first three runners, so the compressor housing doesnt super heat being that close to the header.