Could of things come to mind. With low oil pressure, rattling, and codes P0012 (Bank 1 over-retarded) and P0022 (Bank 2 over-retarded) after you replaced the water pump, it may be caused if the pump had failed and caused l coolant to leak into the oil. If so, this created a "milky" sludge that  clogged the VVT solenoids.    As to the rattling sound, if you reused hydraulic timing chain tensioner abd failed to bled it properly, it probably can't  maintain pressure which causes the chain to slap against the guides.

This always happens to me on my 09 MKX. Rust on the rims.    I pay my mechanic to sand the rim and then apply a tire sealant to the rim to prevent leaks. Have no problems with this process.   Some mechanics' don't want to do this so make certain it's on the work order and verify they will do it; even if they charge extra.   Learned this the hard way years ago. Tires slow leaked, continuously. Took it back to the Ford garage and had them take off the tire, sand to rims and apply sealant.   Mechanic sanded the rims but didn't use sealant. Still slow leaked.   Back to Ford and they tore off all 4 tires and applied sealant.   Amazing how cooperative the service personnel can get when you ask to speak with the owner of the dealership about who should pay. (Make certain the specify both sanding and sealant on the work order.)      

Did the same thing when I had a tire that couldn't be patched. Old ones had about 10k on them, so I had my mechanic pop on 4-new 245/50 R20 Pirelli Scorpion Verde's. New ones are actually smoother and quieter than the one ones.   I'm particular when it comes to tires or brakes. I want the best at all times. (Could be the difference between life and death.)

As i understand it, the rubber plugs found on the bottom of car doors can serve different functions.   One is to prevent road salt, dust, and water from entering the inner door cavity from the outside.   They also act as one-way valves, allowing water that entered through the window seals to drain out.   They also act as cleaning access. You to remove them to spray out dirt inside to door.    They also alliow mechanics to spray rust prevention coatings into the door's interior without needing to drill new holes.    And lastly for sound proofing. They help reduce wind noise  from entering the interior.   .

While most of the pre 2018 cars used two CR2025 batteries, some standard flip keys or older-style fobs may used a single CR2032. Best to check before buying.   BTW, I've never changed the batteries in my 2009 MKX fob.)There good for the life of the car, like PTU fluid, right?)

I suppose it's possible.     At 60K miles, I would have had the brake lines flushed with all new fluid.  As andyman stated above, pushing dirty fluid back up into the brake system is never a good idea.   The " something rubbing in the front area " could well have been the brake wear indicators, if the new brake pads had them.  Sometimes they come new out of the factory out of adjustment and need to be reset.  They are just a simple metal tab that are supposed to start scratching against the rotor when a brake pad has worn too thin.   Also, " warped rotors " are really a myth.  Unless the rotors were of poor manufacture, they do not warp.  What most everyone calls " warped rotors " is really a build-up of brake dust on the rotors, causing the brakes to chatter against the rotor when you apply the brakes.  There is a simple way to eliminate that chatter in most cases.

All well and good that the dealership is willing to swap you into a different vehicle.   Just remember not to blame the vehicle itself.  Always the problem when buying a used vehicle is you never really know how the vehicle was treated prior to your purchase.   Hopefully you get the right vehicle for your needs with zero problems.   Good Luck.

First of all, you realize this post started 2 1/2 years ago.  Many people on many different forums, post questions and never return.  They think they get their answer and stop.   " Butt Dynos " are meaningless but if you think you feel something, there may be something to it.   There are many reports on-line, either on this forum or the internet on people's impressions of larger FMICs installed, including the CVF Performance FMIC, either on this forum or on-line.  You just have to do a search and see what they say.  Just remember, only pay attention to those reports where the only thing they changed was the FMIC and nothing else.   Also remember that a " 3–4% bump in raw potential power " is meaningless in the overall power increase. Example:  300HP Advertised ( which is not the same as actual HP at the wheels ).  Take 3-4%  of that and you are looking at 3 - 4 HP total increase maybe.  Now, add in a powertrain loss of 20-25% and what does that leave you with in overall gains?   0.75 - 1.0 HP  total increase, at best

So the dealer’s mechanic says the entire rear differential/rear end needs to be replaced, and believes it likely contributed to the original PTU failure, and may have also damaged the replacement PTU that was installed afterward. Because the vehicle has had issues almost immediately after purchase, the dealer has offered to swap us into a different vehicle, and we’re probably going to take that route.   I still think the Edge is a nice vehicle when everything is working correctly, especially for highway driving and general daily comfort. But after everything we’ve experienced, I don’t think it’s the best fit for our situation. We live on a steep, rough gravel driveway in the mountains, and if we’re already seeing drivetrain issues mainly from normal pavement driving, I just don’t feel confident about how it’ll hold up long term for our environment and needs. At this point, we’re probably better off moving to something simpler and more rugged, even if that means giving up some of the comfort and luxury-style features the Edge offered.

Ive seen some FMIC vendors claiming up to 40 degrees air temp reduction with their products.   As far as I know... A 40-degree drop could theoretically provide a 3–4% bump in raw potential power just from the air density alone. Also when intake air is hot, the risk of pre-ignition increases significantly. To prevent the engine from destroying itself, the ECU will retard the ignition timing. By dropping the temp by 40 degrees, the engine can run more aggressive timing, which is where the most significant felt horsepower gains come from.   A few years ago I had a 2010 335i, and just by upgrading the FMIC without any ECU tuning, my "butt dino" felt gains of 15 to 20 hp.   So thats why I want to know, how this FMIC is performing on the ST, but I guess the OP is not reading this anymore    I would be great to have his feedback.