I would think there is a way to fix that TKO600 problem. The countershaft flexes downward away from the mainshaft…. so something like a pillow block attached to the floor of the case with a dished bronze bushing to control the movement and allow it to rotate would stop that. If there is no space to handcuff it to the mainshaft. Kind of like the way you prevent ring gear deflection in a rear end.
I would bet the mainshaft flexes upward more then the cluster downward....thus 3rd gear(in the middle) is the #1 break point. I've only had my hands in a couple TKO's and the mazda M5od that was in my '89 F150. They way they are assembled, there is no real way to install a handcuff(best fix). I don't see putting a bushing in the bottom to support the cluster will do much. Installing it would be a real treat with having to slide the shaft in from the top and installing the tapered bearings on the end.
I think if there was any real way to improve it, that places like Liberty or Gforce would have come up with something by now.
My friend ran his foxbody up to 10.50's before chunking his TKO twice. Even with a soflok clutch, it is still inevitable that it will break. He gave up quickly and installed a GF5R.