Not to many Boss owners on this forum apparently.
I'll try and help you out.
1. Your car came with 5w-50 full synthetic oil, thats what should be in it and thats what you should be using. Also it takes 8 quarts!!! I have had my Ford dealer put in the 5w-20 and only 6 quarts before so you have to specify when you drop it off and ask again when you pick it up. Read your service receipt to check again and always check the dip stick to make sure it's full.
When I bought my Boss salesman told me 87 octane was fine, I have only put in 93 octane no lower than 91 if I'm on a road trip and get find the 93. My car ran better with the higher octane gas when it had the stock tune.If your car has the track key program you have to use min 91 octane.
2. Not sure what to do on this one, I would be afraid to use any abrasives to buff it out for fear it would make it worse.
3.I don't have the torsion diff in mine but I do notice a lot more noise coming from the same area you mentioned, especially with the rear seats down. It is significantly more than my other Mustangs but that is because there isn't as much sound deadening material in the car to keep the weight down. The Boss also started out as a base stripped down GT not a premium model.
4. With the gloss stripes on the 2012 car I've used Mothers carnuba wax and also the Showtime detailer wax with zero problems. You do need to stay away from the matt black spoiler, rocker panels and rear valance. Wax will mess those up, make sure to wipe off immediately if you get any on there. If you get wax on there and notice to late and it leaves white streaking use Mothers Back to Black to restore it.
One thing that I highly recommend is that when you wash your car next clay bar it right after then put down sealer and glaze, polish and then a few layers of wax.
There are some really good write ups in the detailing section about what some guys do for their cars so check it out. I will sometimes spend anywhere from 4-7 hours just detailing my car. If you would like a step by step send me a PM and I'll lay it out for you.
The Boss is an amazing car have fun with it!!! Any plans for any mods?