You are unlikely to see any noticeable difference in power with a drop in filter replacement, that is assuming that your current filter isn’t super clogged up. The stock intakes and filter are fairly efficient. I have a 91 F-150 with the 300 six cylinder so I know the pain of being super slow.
You don’t need a tone generator on each end, just one will work
Probably not, the in-tank low pressure fuel pump feeds the high pressure pump via fuel lines. The reason people say it’s hard on the fuel pump to run the tank low is that the pump won’t be fully surrounded by the fuel in the tank and will run hotter/harder. This shouldn’t impact the fuel supply to the HPFP, but it’s still not an ideal thing to do. That said, if you’re regularly running to the point that the car dies, I could see that causing an issue.
I recently scrapped various items from my personal junk pile. This included 2 dead engines, a few old exhausts, a tailgate, some rims, and various other junk metal items. All together it was over 750lbs of recyclable metal, and the total the recycling yard paid me was $40 usd. Since the value of a broken engine is low/almost negligible, I’d consider it a service that the mechanic will probably dispose of it for you.