From the top:
Once the summer heat hits, switch to 10W30 grade oil.
Replace the Bosch plugs with NGK or AC Delco ones. If you are looking at light mods go with the TR55'*, however if you are looking at forced induction (turbo, CSC, nitrous) then shoot for the TR6'*. Above all make sure they are properly gapped
Depending on where you live, those 4 holes you drilled into your tstat may be a bit much.
As for plug wires, Taylor or MSD will do you just fine. I went with MSD to add to my MSD coil setup. That leads us to coils...they cost about $120 and to the average "Joe" thats a waste unless you are planning on going for the big time later on.
You switch to Dex-cool? Did you flush the entire system first?
Gutting the air box is a good start. You can move on to a CAI system from this point. Your choices are domesticperformance.com or ebay. If you can find one, look for the "Pro Zen Motorsports" ram air intake for a Bonnie. I can't complain about mine much because it touched the back of the headlight.
Now for your removed CAT...VERY BAD BOY!
Don't do that, you lost a lot of torque and killed some lovely smelling flowers that way.
Get yourself a new high flow CAT, you will gain back mucho torque and maybe hp.
A transmission cooler is always a good idea. Summit has a nice cheap one for $40 that I just ordered.
Did I cover most of it? I think so.
I'm here if you need more help.