In regards to the engine bay cover, mine is doing the exact same thing with the air intake piece that has fallen off and the cover not sitting right making the oil cap not being positioned right.
I read a thread on another forum the other day but can't remember where or what forum as someone had the exact same problem as you and me. I do remember however that it could be to do with the rubber grommets on the underside of the cover that may cause this? not sure how far to believe this as i haven't had a look for myself yet but it mentioned taking the cover off and making sure all 4 rubber grommets are sat where they should be correctly and then replacing the cover.
You could check this and see if can help you in some way as thats what i plan to do but i think i may be something more than that as in lugs? etc as mentioned above.