Slave cylinder for the clutch is on the driver's side.
I have an 04 6spd. and the interference is between the starter bulge on the back of the bellhousing, the pass. side spring shackle, and the firewall - at least with the MBRP 3.5" downpipe. It fits, but is within 1/4" or less of all three of these at the same time. Try the MagnaFlow 17927, it's what I'd try if/when doing it over.