Compustar non remote starting issues

Me and a buddy just finished w/ my compustar install the other day (CM3000 FM Unit) on my 05 WRX STI.  2 strange things that's been happening... everytime I press on the clutch, my compustar makes a "click" noise and maunal start doesn't work, I would usually have to play with the ebrake and lock/unlock so I can start up the car manually.  Strange thing is that remote start works awesome no problems at all, it's just those few times when I cancel reveseration mode. 

Here's some background on the install...

1) THe Compustar wire that provides a ground during remote start is connected to the clutch switch. (When the clutch is pressed it sends out a ground.)

2) The NPS on my STI is grounded in neutral.  The NPS connected into the brake shutdown wire for the Compustar brain and is diode isolated. (The brake shutdown is a positive trigger, so if it sees +, it'll think the brake is depressed when the car is in gear, and it won't start.)

Everytime I press on the clutch it sends a ground to the compustar and that's what probably making the noise. If I put in a diode (anode on the clutch wire side) that should should stop the clicking noise.   Do you think this has something to do w/ why manual starting doesn't work right?

NPS = neutral position switch and I have a Subaru Impreza WRX STI.... sorry for not carifying.

I do usually have my foot on the brake when setting reservation mode.  How should I be connecting the relay?  I'm fairly new at this 12volt stuff.  Is it a better option then connecting a diode?  Thanks!

How do I switch my compustar between manual and automatic mode?  Since my car as a neutral position switch and is hooked up to the e-brake I should have to worry about reservation mode anymore.  Thanks!