man I feel for you on point 2.
The only thing is can say is to pick a point along the crack about 1/2 way and push with your finger and see if one side moves as you push....that would tell you for sure if it is in fact a crack or if it is a scratch in the paint. That bites!
The exhaust is a tough Q. I'm getting headers also and I've decided that the stock exhaust stays on the car for now....it is such a pia to store & transport.
I have a 90 & I use my car alot so it is not like it's a NCRS top flight car and they made so many 90's that I doubt my driver will ever be more than that. If I get another exhaust I'll toss my OEM stuff or give it away....ya can't save everything...no room for all of it. The stock answer is "save the parts" so you can return it to stock, but if you drive the car my Q is: does that really matter after 50k miles????
Only you can decide if it's worth it to save the whole exhaust system....I'll proly save my manifolds for as long as I have room but eventually I know there will be a choice. I'm not renting storage space to save stuff, no way.
Tom