remote start issue in 2003 honda s2000

The other thing that comes to mind is re-program your immobilizer bypass module -- perhaps this is somehow interfering in the remote starting process.  The brain is working to SOME extent, in that it'll arm/disarm, lock/unlock, and allow you to remove your key and keep the car running -- so the relays internally (brain) are working to maintain ignition and accessory power. 

The brain is getting caught up in the starting process -- just double check to make sure your sequence of getting out of your car is correct (with the E-brake, clutch, etc) and if this problem persists despite that, I would go under the dash and re-program the bypass unit (IF it is one of the ones that can be re-programmed) 

Also, nothing beats just double-checking all the wiring from the brain to all the pertinent wiring locations to make sure all things are connected.  The whole issue of the remote starter ceasing to function AFTER he changed to the new, smaller battery may be simply coincidental,and have NOTHING to do with loss of programming or anything like that.  There very well could be an issue with the wiring of the brain -- certain types of inferior quick wire connectors have a bad history of failing over time.  Soldering wire joints are the best (if done right, that is).

Yep it works with the clutch in...I  basically followed what you said

started the car, followed the "remote start process"

while in the car, turned the ignition off, open close door,

arm,

press clutch, press remote start button,....3 seconds, engine comes ON! What do I do next?

I looked at the clutch and honestly saw one plug. Regardless, there is a wire connected to it and its a white one.

In addition, there is a Diode wired into that wire.

I thought for a second, as well that it might be a loose wire like someone mentioned before, because I stayed in the car and pressed the remote starte button. As the car is trying to start, I stuck my foot under the dash in the direction of the wire of the clutch and it started on its own. I went back under the dash and checked all the wires and still no luck. any guesses?

Sounds good, but how do I do that? Ive read the manual and no where does it say how to remprogram that feature?

Do I  just follow the steps to the "tach signal learn" or...