1: Is there a better aftermarket or year model ECU that will improve performance?
On a stock car, I don't think any aftermarket ECU would make that much of a difference.

2: Can I advance the timing and if so, How?
Rotate the distributor a few degrees backward, I think.

3: Why the hell is "S3" constantly blinking?
I don't know what S3 is

4: Waht exactly is the S4 shift button? Does it increase line pressure for higher RPM shifting?
Dunny what S4 is either

5: Does anyone have any extra valve cover nuts they could sell me?

6: what is the wheel size (4X100 4X114) ?
Bolt pattern? It's 4x100. Wheel size I'm guessing is probably 14x6 or 15x6.5 or something like that.

7: how good is the stock Suspension?
Good enough for daily driving. It's old though.

8: Where the hell do the rear speakers go? and what size are the door panel speakers?
Don't know much about 2nd gen integras, sorry.

9: Is there an easy way to remove the front bumper (gotta paint it)
On a 3rd gen there's just a bunch of bolts on top and some clips in the fender well. It might be the same...

10: where can i get a stall convertor?
Don't know, sorry

11: What size is the stock exhaust pipe?
Don't know that either... 2 3/8"?

12: and finally, should i paint the steelies Gloss black or Gloss White? (The car is Red.
Black.