Reloading the stock file from the SCT X4 to your car will have no effect on the vehicle count. You have to have a different VIN number to cause that to happen.
In fact, SCT recommends you reload the stock file in the car before you upgrade the firmware on the X4.
Now whether you should...
Since you're going to put a blower on it, I assume you're not interested in road course or autocross events.
What will you be primarily using it for? Dragstrip or street?
If dragstrip then I think the Boss would be better because of the lighter block and with a blower you'll have more HP &...
At higher speeds the high centrifugal forces would keep any loose object pinned to the barrel of the wheel.
When going slow, a bump may be enough to dislodge it and make the noise.
Easy enough to check by jacking up that corner and spinning the wheel.
That's great that things quieted down.
As long as the grease doesn't get on any part of the rotor that the pads contact.
To find the root cause, I suggest you raise the rear put the axle on jackstands. Take off both wheels/tires (for safety's sake) and then put it in gear at idle.
Then...
Did you check the caliper clips for wear? The rotor may rub against them occasionally. Also, check if your rotor is centered in the caliper. If it's not it may have a greater propensity to rub against the caliper clips.
For HPDE I run square 18x10 Apex EC-7 ET43 wheels with 295/40-18 Falken RT615K+ tires.
With -2° camber I run 3mm spacers up front. The newer EC-7 are now ET40 so I wouldn't need spacers with those.
What will you use the car for? If you're going to do lots of autocross or especially if you're going to do HPDE then a bigger radiator such as a Fluidyne or Kenny Brown triple pass radiator may be in order.
Ford Performance also has a higher volume water pump too. 5.2L "GEN 2" WATER PUMP KIT...
The video above is good one. Make sure you read the comments about it too. There are some good nuggets there.
I assume you either have or will be getting an aftermarket cold air intake to feed the new intake manifold. I recommend the JLT Series II.
Since the new manifold holds the throttle...
The Boss (Roadrunner engine) OPGs are the same as the Coyote.
The Gen 1 Aluminators since 2013 came with the CobraJet oil pump that has the billet OPGs.
Supposedly, between 2011-2013 only the supercharged Aluminators came with the CJ oil pump and the NA Aluminators did not.
Congrats!
As far as protecting the engine, replace the crank gear and oil pump gears with billet gears. The OEM gears can shatter if you hit the rev limiter. It all depends on how you drive it. For spirited driving and occasional runs on the quarter-mile you're probably ok. But if you plan...