I know these are quite old but I got too interested not to reply ha
Scramjets will never be used for anything other than missiles, possibly on spacecraft, but certainly never on commercial planes. Firstly they must use a rocket motor to reach a high enough speed to begin supersonic combustion, once started all the ones flown so far have run for a very short amount of time. Aside from this, the main issue is payload weight. They simply can not be designed to efficiently carry weight particularly to travel any distance because the amount of fuel required becomes hugely prohibitive.
I'd be extremely surprised if you didn't see it again at some point. All it needs is the correct economic situation and state support (i.e. a pan-European project) and SST can become economically viable.
No one will design a commercial plane that cruises at transonic speeds. The drag between Mach 0.8-1.2 is significantly larger than above and below those speeds. You design a plane to cruise at subsonic or supersonic speeds not in the middle.
Airliners as you know them now will not go much faster than they do currently, they will only do it more efficiently.
The SR-71s weren't pushing the envelope "just that little bit further". They were rewriting the book on super....supersonic aviation!
Since then high temperature materials have come along a huge amount too, not to mention the Russians would be much more willing to sell their finest Ti when they know it's not going to be used to peek over their fence!
The first of your points is fair enough for a plane flying THAT fast, plus the skin was actually rather thin in a lot of places. The markings around the cockpit etc are there to warn ground crew not to lean on them in case it's bent!
The third about the misfiring, that's a problem they actually solved after it was discovered. They developed flight control hardware that could detect a inlet unstart before it happened and compensate accordingly.
Unless I'm getting confused between something else you're talking about the D-21 which was launched off a still experimental A-12. That was a ramjet and it didn't explode when it hit the shockwave, it seperated badly and hit the mothership causing both to crash. The crew ejected and survived but unfortunately the navigators pressure suit leaked and he drowned.
Scramjets don't work at less than 3,500mph
The "G" at 5000mph would be irrelevant. It's the acceleration that causes that stuff, and since you need a rocket to accelerate to the appropriate operating speed, yes there would be significant acceleration on your body! Possibly beyond Space Shuttle levels!
The cost in fuel per hour would be nothing, literally nothing, in comparison to the maintenance costs.
Although it would be cool to have your own fighter jet haha. I don't know of any supersonic light transport planes though...