Most times when the factory door panels get 'waves' in them because someone had the panel off and didn't install the water/dust shield to the door correctly or left it out completely.
Now note I said 'mostly' so don't you people jump on your key boards with 'I left mine off 20 years ago and mine are good' posts

and that dipstick issue, (not you
@limp ) is yours stock with a Ford part number? It is yellow like stock. Aftermarket headers sometimes do not play well with stock dipstick tubes and installers just grab the tube and man handle it out of the way, that usually kinks the tube so it won't go all the way down into the boss. I used a hand tubing bender to fine tune mine.
And on the 'over full' thing, there is a TSB I believe, can't remember what it said exactly how to deal with it but the common method is to fill with 5 gts oil, new filter, run the engine for awhile, the check oil, mark the stick where the oil level is and your good. Mine is a 1/4 " above the full mark for example.
Exhaust droop, looks like there is 4 pieces between the headers and the mufflers, you may be able to loosen the 4 connections and using a floor jack, 2x4 to push the pipes higher and tighten the connections.
Oh and that 'ticking' noise may be a loose header or blown gasket so check that out before messing with adjusting the pipes.
Disclaimer: this is based on The Roadkill School of mechanics and not on any actual real mechanical training. Use at your own risk.