For the "measuring" of the temple, he used the scriptures that were available at the time to determine this. No Catholic leadership was involved in that, as that would cloud the Scriptures altogether.
As for why I talk about the historical timelines, a book by Edward Gibbon called "History of the Decline and Fall of the Roman Empire" exactly explains how Revelation, Daniel and Matthew 23 were being fulfilled (at the time, from 1776). That, and many theologians who had fantastic works were all from the 16th-20th centuries. Mind you, Gibbon wasn't a Christian, despite writing something that exactly explained the historical fulfillment of these three books.
When it came to the Ekklesia fleeing to Pella for the Jewish-Roman war, the Nazarites (400 years before Christians) never did what you described. Worshiping under bishops is not the same when you look at the biblical definition of it from what I've read. On top of that, the Eucharist is actually a blasphemous ceremony (for it brings the authority of the Creator and Messiah to naught, which you don't do). Peter and Paul tried to make it work, but after Peter and Paul passed away, Lucifer took over and completely mucked it up, thus making it his seat (which is why he selects the Popes he does, probably through the General most likely since 1798).
As for the rebellion, yes, it was a rebellion performed to save the Saints from the persecution of Catholic leadership, as the Pope was reigning over the entire known world at the time (this was before 1798 when the General took over). Not to mention that Messiah allowed the misdeeds of the Roman Catholic Church to fester as a means for people to see who controls us. The "falling away" was more to do with the Pope forcing people who wouldn't worship or obey him to do so or face death (there's a Papal Bull that literally calls for the death of non-Catholics that's still in effect. There's your Mark of the Beast right there in front of you).
As for Messiah not founding a confusion, I agree with that, but the term "Church" is modern day. I use the term "Ekklesia" as a means to distinguish between babble buildings (which is what churches are nowadays) and the assembly (those who follow the Old Testament where applicable, and still followed Messiah's clarifications).
That's just how I see it from the research I was doing on it.