I just wanted to bump this. After a long time of this being open with F5 support I was essentially told that the iApp doesn't support multiple exchange servers configurations and I could try to build it myself or pro service consultants.
If it doesn't work it shouldn't let you even try to create a second iApp so you don't break your production/working environment like I did. I'm really surprised this doesn't come up more often. I can see all kinds of reasons to create a second even without multiple customers.
So if anyone ever run into this and figures out how to fix it please post. I pretty much have to leave those customers on Firepass until its fixed or we just take F5 out of the picture and put these servers in a DMZ.