2008 Honda Civic Si Sedan Alarm/Remote Start

Yes, attach door pins to to the Vipers (-) door trigger input.

All four door pins can be found in the Green 42 pin

The DRIVERS DOOR is a GREEN (-) at Pin 37,

Clutch bypass should be pretty straight forward.  I used a Compustar 5200-s remote start.  It has a (-) Start output  rated at 250ma.  I went directly to the orange wire in the yellow plug at the clutch pedal.  I also attached the R/S's heavy gauge (+) Start output to the heavy gauge yellow wire (+) Start at the ignition switch, although I heard it wasn't necessary.  No problems, the car is working fine but adding a relay to the (-) Start as Ted suggests won't hurt a thing.  Especially since your units (-) Start output is rated at 200ma.

Did you find the hand brake wire?  It's in a White plug on the right side of the steering column.  It is a very light blue color.

Yes, that will work nicely.  Don't forget that in manual transmission mode, you must be in Tach mode and connect the R/S to a tach signal.

Also, as Ted pointed out, there is a procedure to put the car into Reservation mode to enable a remote start.  This Reservation mode ensures that the car was left in neutral with the doors locked.  If any door/trunk is opened afterward the reservation mode is cancelled and the car won't attempt a remote start.

the car has negative door lock triggers.

you will only need one relay if you wish to have Driver door priority access. (unlock driver door first, then the rest of the doors)