I think you're looking for QEMU, not LLVM.
The low-level virtual machine in LLVM is that, after converting the higher-level C and C++ language input into an internal low-level representation (as a stage in the normal compiling process), it can then save this low-level representation and execute it on a JIT compiler (which thus acts somewhat like a virtual machine). This JIT compiler does a substantial amount of optimization, and so I expect it would be difficult to instrument in quite the form that you're thinking of -- in particular, it does not do instruction-by-instruction stepping through the execution.
QEMU, by contrast, is an open-source emulator that does instruction-by-instruction stepping through of machine code. It already contains a certain amount of ability to instrument code to look for certain conditions, in that it can connect to GDB and set watchpoints and so forth, which are implemented in QEMU itself.