I just replaced the clutch master cylinder yesterday in the 2001 SE -- the OP's pics and descriptions helped as did the FSM.
I didn't need to remove the seat, nor the clutch pedal or the two or three colored switches. Did remove the clutch safety switch, and then carefully bent its bracket 45 degrees down to allow the master cylinder to come out and the new one to go in. The upper (of two) mounting bolt for the master cylinder was the biggest pain of the job.
After gravity-flushing the brake fluid, I used the fish-tank tube from the bleed-port to the fluid reservior technique for bleeding. Took 100 or more pumps to clear the fluid.
The replacement clutch master cylinder, $35 from AutoZone (PN 51370), was a LuK that was identical to the original 2001 LuK part that was removed.
Fixed Up a white 2001 P-code SE Sedan
including rebuilding the SPI (see my threads)