Progress:
With revision 2191 I've improved the performance of LoadByteCode to be about 4 times faster, for a scenario like this:
usedFunctions.GetLength() is equal 40001
module->bindInformations.GetLength() is equal 0
module->scriptFunctions.GetLength() is equal 20000
engine->scriptFunctions.GetLength() is equal 60019
On my i7 this takes about 1.41 seconds to load (before improvements it took 5.63 seconds). The total size of the pre-compiled bytecode is about 4MB.
So far the optimization has been concentrated on the matching of registered functions/methods done in ReadUsedFunctions. But I'll search for other things that can be optimized. I'm sure it will be possible to bring down the load time even further.