The burning smell you are smelling is normal. Also you don't want to be slamming the car around like it's got 10,000 miles on it. Drive it normal. The best thing for it is to go on the highway then take a city street. Stop and go kinda street to where you can go from 35 to 55 then back down. You have to break the engine in before you can start hammering on the engine.
I say this after a buddy of mine, master mechanic for almost 30yrs, told me how to break a brand new engine. The limp mode problem is beyond me but you might be doing the opposite of what I just said and could be causing the issue. I don't know to be honest.
The hood issue. I've noticed I can't just softly close like my last Z. So I slam it shut, not hard but I drop it from about 2 feet. I'm sure it's just the new seals that are creating the issue.
Good luck with her!!!
Oh yeah I bought mine with 17miles on her...now sitting at 1021 after a month..