IPhone 5 won't back up/update

I have an iPhone 5 and a MBA. My iTunes library is on an external harddrive.
I need to clear up space on my iPhone as well as back it up.
I can't update it because there isn't enough space on the phone.
I can't clear space because most of it is pictures, which won't transfer to iPhoto (I keep getting an error).
I can't back it up because because it won't backup to my external harddrive. There is no option for me to point it to my external drive, and the iTunes library I have opened while I'm trying to back it up is already pointed to the external drive, but it still tries to backup to the regular harddrive, which is full.
I'm not sure what I'm suppose to do here.

Hey Dub180,
Thanks for the question. I understand you are experiencing issues restoring from an iCloud backup. The following articles may help to resolve your issue:
iCloud: Troubleshooting restoring an iCloud backup
http://support.apple.com/kb/TS4036
iCloud: Restore your iOS device from iCloud
http://support.apple.com/kb/PH12521
Thanks,
Matt M.

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I've posted this issue in the iPhone forum (https://discussions.apple.com/message/18962855?ac_cid=op123456#18962855) but I'm having a series of overlapping problems related to my iPhone 4 and iTunes so I'll post here as well. Here's the long diatribe
1) 90% of the time that I try to open up the "Music/iPod app" on my iPhone, it crashes before it loads anything viewable or listenable.   5% percent of the time it simply loads an empty interface with no music. I know that there is music on there becuase the reamining 5% of the time it does work, and even when it doesn't work I can hit play on my headphone remote and listen to tracks. These symptoms are present regardless of whether I have iTunes Match turned on or off on the phone itself (yes, I'm a paid user)
     1A) During the 5% time that the Music/iPod app does work, iTunes Match, or iTunes in the Cloud, or whatever the **** ya wanna call it, doesn't work in any stable shape or predictable way.   Although I can "see" my tracks, any attempt to download them to my phone (even with WiFi connection) usually causes the phone to get confused about what it's downloaded vs what it hasn't. For example, if i choose an album and click download all, then it'll start playing the songs as they come in (sometimes with hiccups, presumably from unfinished downloads).    Fine, no problem. However, even if all song completely download as intended, I will eventually get an alert on the iphone saying "can't download track from the cloud" or "error downloading track from cloud" (I don't have this alert committed to memory so I'm paraphrasing).   When this happens and I go to the Music Store to view the download que (which is somewhat odd since I'm not buying the tracks, but I digress) ALL of the tracks that I have selected to download show a status of "waiting" even though ALL of them have actually already downloaded and I've listened to them. The only way to alleviate the neverendign cycle is to do a restart on the phone.
2) I wanted to back up my phone and do a complete restor to factory setting but I can't sync through iTunes. When I connect the phone with the USB connector, iTunes sits in a perputual state of "Syncing iPhone (Step 1 of 5)" while the never ending sync clock spins at the top of my iPhone.
     2A) If I disconnect the phone manually (pull the cord), the syncing arrows still spin. The only way to stop it is to do a restart on the phone.
     2B) I've tried deleting previous backup files and manually backing up with no success. Someone on the iPhone forum suggested manually deleting from ~/Library/Application Support/MobileSync/Backup but that path doesn't even exist on my system. Sounds like that could easily be the culprit but even a new install of iTunes isn'ts solving the problem and it raises other questions of where my backups are currently residing.
3) When the phone is connected to my laptop with the USB dock conector, iTunes says that my 32gb iPhone 4 is over capacity by 3.1gb.    However, when looking on the iPhone itself, it says that I've used 17.4GB and have 11.2 available.
Notes which may or may not be of significance:
A) I had a corrupted iTunes library on my external hard-drive a few months ago.    I don't know if this was the cause or the result of the above problems but that issue has since been taken care of. Sadly, my phone problems still persist.
B) I've just learne of the application iExplorer and was thinking of using that to address any bad iTunes library that might exist on my phone. However, because I can't back up my phone yet (see 2 and 2A above), I'm reluctant to use any third party solution just yet.   I would love to know anyone's feedback on this product however.

I just updated my iTunes to 9.2.1 and my iPhone 4 backed up just fine. Did you make sure you did a restart of you computer after update. Check in your iTunes prefs and see if you have your auto sync disabled under devices. Let me know what happens

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