Hey Boback,
Glad to hear from you.
1. There could be a significant difference if you trade the smaller time frames as M1 and M5 (if your broker has some execution problems on a live account). That is why I use mostly M15 and H1. The difference in results could come when you move EAs from Demo to Live. You will need to give the EAs some time to synchronize.
2. Have a look at our FAQ section for some FIFO tips. But trading with Portfolio EAs will be the hardest to go around FIFO because the Portfolio EAs work on one asset and one time frame.
Let me know if there is anything else.