IMessage won't work/isn't up-to-date on iPhone 6 after restore from back-up

Question

So I have been trying to set up my new iPhone 6 since Tuesday and I am at my wit's end. I have been an Apple user for years and am usually good at fixing issues myself.
BACKGROUND: With my iPhone 5, I was having an issue with bookmarks not syncing "Bookmarks could not by synced because the iPhone cancelled the sync" starting shortly after I updated to iOS 7.  I had incorrectly assumed the issue would be corrected with a subsequent update, but that never happened.
iPhone 6:
When I first set it up, I did from the last back-up from my iPhone 5, however it somehow did not complete.  I initially thought I'd lost my 2700 pictures that were on the 5 as only 500 showed in the 'Recently Added', however iPhoto (on MacBook Pro) detected all 2700 on the phone even though they weren't showing, so I successfully imported them from the 6.  When I went to sync the 6, it gave me the same bookmark error.  I tried turning off hard sync and syncing through iCloud but nothing happened (I have never synced from iCloud as when I first tried to set it up after it was created, it created duplicates of ALL of my information and I just never had the time to mess with it.  I figure if the hard back-up works, that's all I need.
That being said, I did NOT intend on having a brand new phone with the same error, so I did a FULL RESTORE and set it up as a NEW IPHONE.  Everything worked seemlessly including my iMessage, however it did not have any of my old messages or recent calls which I thought was strange if that information is associated to my Mac/iTunes account.  I thought the Game Center would have saved most of my info from my games, but when I saw I didn't have any of my info from my Lists app, games, and other settings and passwords, I decided I would try a different way.
So I removed unnecessary apps with no info, photos, and music from my 5, synced and backed it up, updated to iOS 8, backed THAT up, and then did a RESTORE FROM BACK-UP on the new iPhone 6 from that latest back-up.  Despite that, I have discovered that the messages and recent call list that DO appear on the phone only go through MARCH of this year... I am so confused as to how the most recent back-up would have only backed up info from March... My games data is up-to-date.
I THOUGHT everything was working with the exception of STILL having the same BOOKMARK SYNC ERROR, but I just discovered that my testing/iMessage does not work at all.  I go to send a message, and it just shows the blue bar loaded 3/4 of the way, and never delivers the message.  My boyfriend confirmed that he cannot send me messages either, which makes no sense because the phone was set up under the same phone number and emails as my iPhone 5 was.  I really don't have the time and/or patience to go into Apple, but after spending ALL day yesterday trying to re-set up the phone thinking everything worked, I am quite exasperated.  I have been using Apple products all my life, and I have NEVER had this much trouble.
I never had any significant software issues until iOS 7, and the fact that they are still ongoing is quite ridiculous.  It's getting harder and harder to defend Apple and their quality products if they don't kick it into high gear and fix these glitches! 
Any help would be greatly appreciated.  Thanks!
P.S. I did some reading on how iBackUpBot is supposed to fix the bookmark syncing issue, but it seems a bit technical.  Perhaps clearer instructions would be helpful.

Answer 1

Well, right now, Apple is getting loads of people who are trying to download the new update. My iPod is doing the same thing, so, just wait an hour or two and then try again. It may take a while to veryify the update, and even longer to actually download it. Some people at my school updated their OS in study hall, while others were having the same problem you were. It should be fixed soon, just relax...