If you don't have any interesting control operators like call/cc, prompt/control, etc. then it should be possible to track stack-like control patterns after CPS conversion through the compiler and through DWARF (or a custom debugging format). Unless I am missing something it seems that the control operators are the problem, not CPS.
Certainly, that's true! As I mentioned in my other far-too-wordy response, though, if you just CPS convert and run a program, it will be far too slow (5x the funcalls != 5x the fun...). So, it's the combination of CPS conversion and later optimizations --- paired with whole-program compilation --- that make it so hard to debug.