Factory5

i had a 5 speed soarer and it got rear ended so i bought a new one and now in the process of a five speed swap. Everything was going great till i got to the clutch master cylinder/pedal box and for some reason it doesn't seam to fit ive been working on it for the past 4 hrs and im completely stuck. The threads on the master cylinder dont seam long enough.i was thinking about just cutting all that carpet away and see if that worked but not sure what to try next. Any ideas?