I am sorry to say that LLVM just isn't very fast as a JIT compiler, it is better as a AOT/static compiler.
I have run into the same speed issues in my llvm-lua project. What I did was to disable JIT compiling of large Lua functions. llvm-lua doesn't have lazy-compilation support turned on since LLVM requires too much C-stack space to run from Lua coroutines.
Also if you use this in your program's main() function:
llvm::cl::ParseCommandLineOptions(argc, argv, 0, true);
It will expose alot of command-line options from LLVM like '-time-passes' which will enable timing of LLVM passes, to see which parts of the JIT compiling is taking the most time.