GSR = not an EK
I have a generic 1-piece 3" CAI pipe with my LS swap in my 98 DX hatch. I had to cut out the hole in the sheetmetal behind the headlight to get the pipe through. There is a circle-shape depression in the metal that is perfect to cut open with a sawz-all or dremel. then I got some of that door-guard stuff and put it around the raw edge so it looks better and doesn't rub a hole in the pipe.
The only other option I can think of is buy a 99-00 Si cai, it might fit easier but still require a little tweaking for the GSR t/b location.