you can also check out bulldogsecurity.com
they have wiring diagrams that you can use off of there
site. I installed a remote start from them in my '01 Taco. The install was a lot easier than my previous '01 Chevy S10 that I had the starter in. Good luck, I can try and answer any questions that you have but I have only used the bulldog products.
really dont think remote start is a good idea on a manuel. That being said, If you do it you can set it up with a few pin style switches around the shifter that will only let it engauge in nuetral. As far as disableing the clutch start cancel you have a couple options you can do whats stated above and wire pass it. Or if your alarm has a output that can be triggered right before start up you can trigger the clutch start cancel switch on you dash that way you dont loose cruise control. if you dont have that switch you can cunstruct something to do that with a relay. Good luck