First of all, I want to say that it's awesome that you're taking on this large of a task. Imo, the attack code is nowhere near Live, but I personally think a lot of this has to do with random number generation. Live is random, but like you would think it should be. Emu seems to get randomly generated numbers close to each other, but still in waves (damn computers...) The best example I can show, which may just be a general issue in the code, is when lower level stuff can hit you, if it does hit you, they will hit near max damage almost every time, where on Live, if it does hit you, it will be for crap.
In any case, good luck working out the kinks