Impressive build. A couple thoughts:
1) The single plane intake is most definitely going to cost you power down low! It is really the wrong choice for your build. Single plane manifolds don’t make more power until 5000+ rpms, and they are notably down on power below that.
2) The Mustang cam is the same as the tbird cam. This cam is made for idle quality and emissions on a motor that was out of breath at 5k rpms. You now have a cam that wants to make power at 3k rpms, heads that want to make power at 4-6000rpms, and an intake manifold that wants to make power at 7500rpms. The result is the intake kills your bottom end, the cam kills your top end, and the heads, can never perform the way they should.
3) I’m surprised by the issues with the truebendz kit. I have used a number of their kits before, and while they require some time and tweaking to get everything lined up properly before welding, they have always fit and cleared the gas tank and rear suspension for me without issues. The fuel tank changed for 92, not 93, so it should fit your car, unless someone put the early style tank in there. One thing I always do on them is actually weld the pipes to each other where they go through the gas tank area. This keeps them close together to clear everything, but since they are welded to each other, they won’t rattle.
4) For the motor mounts, flipping them side to side will move the engine back 1”. Since you said they are in the more forward position, they are probably in the stock location. I don’t know about the AJE K-member as I have never worked with one of them, but one thing to keep in mind is moving the engine back can create clearance issues with the headers, so keep an eye on that if you try switching them.
6) I probably wouldn’t change the rear gears. 3.27s might be a slight improvement, but not enough to justify the work involved, and if you like cruising on the highway, the 3.08s are great with the M5R2. What I would do, given everything you have already done, I would swap the cam for something with around .500-.550” lift and maybe around 230@.050” duration and a 112/114LSA, then ditch the single plane manifold for a good dual plane. With those 2 changes, you will have heads, cam, and intake that all jive and work together in the 3000-6000rpm range, and I think with the M5R2 trans that will really make the car come alive!