OK, I found the thread that gives the info on the cut-wire trick for the trans.
torque managment, how to fix the 1-2 shift burp - PT Forums - The PT Cruiser Enthusiasts and Owners Resource
The Kenne Bell Optimizer is put on/in by the seller, you have to send in your computer and they send it right back fully programmed. There's two drawbacks to the optimizer: 1, you have to use premium fuel to get the benefits, and 2, never let the service department at a Chrysler dealer "flash" your computer. If they do, you'll lose the programme that was put in by Kenne Bell.
I've never done the air-filter upgrade with the white silencers, but I've read and heard that it does help. I believe there's two white silencers in the air box that are removed plus I think you add a bigger intake pipe at the area where it draws in air from the hole in the fender. Also a more free-flow air filter itself is recommended.