1. Is there a way to do this?
2. Is it a good idea to do this after a few simple bolt on's ?
3. What are the negatives to this ?
4. (This is my shot in the dark question) Will it learn that I have 3.73's instead of the stock 2.73's?

 

1 Yes, pull two fuses. PCM BATT & PCM IGN for a few seconds.
2 Does not hurt.
3 None I'm aware of.
4 No.

 

This wont make my damn alarm stuff kick in will it? The anti-theft for the radio?

How long will it take for the car to learn all the new stuff?
*Forgot earlier to ask about 160* thermo, but I'm thinkin it will not learn that....

 

The car's computer is not like a regular computer. Stuff isn't "plug and play" on the car. You have to physically reprogram the pcm for the mods that require it.

There's no reason to reset it unless you really want to. It just won't change anything if you do. (at least nothing you will feel/notice)