Well, turns out I got bleeder-type jets  .....So at the moment no rejet for me.

I have two questions though.

                 What is the part number of the #40 pilots (for a '97 btw), 'cause my local dealer (Fun Bike Center) only had bleeders.

                 Also, what is the stock setting on the air mixture screws?

I am temporarily going to set it back to stock since I can't get it to run with just the new mains and the old pilots. (any guesses on that?)

http://gstwins.com/gsboard/index.php?topic=5460.msg44409#msg44409

You should still be able to run with the mix screws out 3 turns, irregardless of pilot jet size.  Set them and leave them.  Control your desire to fiddle with 'em; restrain yourself.  Otherwise, set them to 1.5 turns out, that should be lean enough (or one turn).

I couldn't get mine to run after I opened it either, but I figured why bother since I was going to get it jetted right anyway.

After getting everything all set back to stock...I realized that my floats were not set correctly. I was, for the most part, running on one cylinder the whole time 

But, now it runs better than it ever did 
So, probably sometime next week I'll get it all set up for the re-jet.

I guess I'm just a n00b...but I can't seem to find the pilot on cycle gear 
I'm probably just over thinking it all. 

No, you're allright, it's not listed on Cycle Gear's site, nor will it be, because they have always been a dirt-oriented store.  You need to go in there personally (as did I) and hopefully you will get someone who knows, or understands, what you are talking about.  Non-bleeder type pilot jet, p/n: N151.067-40