This small set should cover pretty much everything needed. As far as I can tell the grab handles are torx plus 30 which sould be in your bronco tool kit. I can double check on size and inclusion when I get home.
https://www.amazon.com/dp/B004UC9WJE?ref_=cm_sw_r_apan_dp_MK5ZW85WXD3AANWB7A6R
I took my muffler off a few weeks ago and have been driving like that without too much of an issue. The Flowmaster is louder behind the vehicle than when I was dumping at the axle but much quieter in the cab now (hard top). It's loud when you get on it jumping on the highway or if you gun it at...
My price after everything was exactly what the build calculator said, but it really all depends on which dealership you go through.
Make sure you get your final price in writing and it's worth checking with members in your area to find a dealer with no ADM.
Does your garage have any ventilation? I had the headliner of my F150 fail after a week in a garage with no ventilation. I'm not saying this is definitely the problem, but it's worth looking into.
The stock muffler is just too damn quiet. I'm used to being able to at least tell that the engine is running. I plan on adding an axle back or possibly cat back at some point, but I'd like to hear a few in person first. In the meantime, I can now hear it when it's on.