Need Desperate Help Regarding iPhone 4 Sync Issue (PC, Win7)

Question

I'll attempt to make this question as concise and fully informative as possible. I have an iPhone 4 Jailbroken running firmware v4.3.3. I typically sync my phone with my PC on a normal basis until this past October I bought a new SSD and had to re-install iTunes on my C drive. As you know, a re-install means that any re-sync with a fresh iTunes install means that the phone will basically wiped clean. Since the new iTunes install I have regularly been "Backing Up" the iPhone,(but never synced it) however this is not a "Sync" of course, but I figure it still beneficial to do. I believe I have the following options and/or issues to deal with:
1) Is there any way to "reverse-sync" the iPhone to the PC, instead of the other way around? I kept the old iTunes operating files but I am not sure which ones I'd need to copy over to which folder to make a "current" sync happen, or to "fool" iTunes into thinking nothing has changed since the fresh install.
2) I realize a "restore" will erase the jailbreak, but what if I choose "Restore From Backup", will that also erase or reset the jailbreak?
3) I am mainly concerned with calendar appointments, my apps with invaluable information, and notes. Everything else such as music I can simply re-sync if I have to.
In essence, I am trying to do a up-to-date sync with the new iTunes install and loose as little data and information as possible (or none at all). I have apps installed such as iFile that hold many files within the folder tree structure of the phone that I cannot afford to loose. I'd be willing to make backup copies of all these files if there is a viable solution for me, which Im hoping somebody can recommend to me.
If there is a special app or PC app that I need to make things run smoother or achieve my goal I am more than happy to install whatever it takes. Thank you for any responses, they are most appreciated.
I have attempted to be as detailed yet brief as possible with my explanation of the nature of my problem, yet feel free to ask a question if it will assist you in further diagnosing and solving my issue.

Answer 1

Let's say I, at this very moment, "Backup" my phone in iTunes.  Once finished, I immediately perform a "Restore from Backup"
There will be no change in your phone, assuming you didn't change anything or receive any messages between backing up and restoring the backup.  The phone will have exactly the content of what was in the backup.
will iTunes have imported all saved phone data into its registry?
It saves phone and app settings, messages, visual voicemail, contacts, Camera Roll, app data.
such as apps, music, etc., since, remember, nothing is there now.  I need to put phone contents on the PC rather than the other way around
No!!!!!   iTunes Store content (apps, music, media) is synced to and from iTunes - it's not in the backup. If you never synced your phone with this computer before, the first sync is  unidirectional from the computer to phone.  If there's nothing in the iTunes library now, what's in your phone will get deleted. In this case, you have to first "Transfer Purchases"  To do this:
1. Be sure that automatic syncing on connection is disabled in iTunes Prefs > Devices > Disable.....
2. Connect phone with iTunes open.
3. Right-click the device tab on left border of iTunes window.
4. Select "Transfer Purchases."  Note that any music/media on the phone that was not originally obtained from the iTunes Store will not transfer to the computer.
It's now safe to sync the phone.  Note that when you select "Sync" on the iTunes page, the phone is typically backed up as well, if you didn't set it up to backup to iCloud instead.
http://support.apple.com/kb/HT1766
http://support.apple.com/kb/ht4946