Hey man, just reread through things, don't know how I missed the bra question.
Leave it off, it will hold moisture on your hood and fenders and cause them to rot. Here's a picture of my "new" car, the right fender needs to be replaced because of the bra that the PO had on it:
You can see where the bra was. I'm going to obviously need to strip the hood and left fender to fix the problem (truthfully, I'm going to strip the whole car once I get into it).
The old cap, rotor and plugs looked just a little rusted, huh?
Do you happen to have the old air box? If it were me, I would put it back on instead of the filter you have there now. It doesn't have a big flow rate, but the colder air from the fender would be better than a little more air that is hot.
Keep it up man, post more once you're done with the tune up phase, I'm interested in hearing about how it runs after you're finished.