iPhone How to safely update to iOS 7.0.4 from 5.1.1 without losing anything ?

I am on iOS 5.1.1 (jailbroken if that matters) and want to update to iOS 7.0.4.
Now which would be safest way for me to go about this so that i do not lose anything like SMS, Contacts and hopefully whatsapp chat history.
I tried in morning with my iPad and it gave me some error when i tried updating in iTunes (using IPSW, shift + update) and then my iPad went into recovery and then i had to use shift+restore with downloaded ipsw and then restored the backup but seems some apps did not restore back, no idea why.

Please suggest.

PS: I will be downloading IPSW of iPhone 4S because i do not have good internet and many a times iTunes update gets interrupted and starts all over again wasting too much time.

WB2Colorado said:

If you're jailbroken you should always restore to the latest version of iOS, restore from backup, and then rejailbreak the device.

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Do you mean to say that in iTunes instead of doing UPDATE, i should instead do RESTORE (shift+restore since i am using IPSW) and it will automatically update iOS 7.0.4 and it will be sort of clean install and then restore my backup (which i would have taken before restoring to iOS 7.0.4) and that should ensure that i do not lose anything ?

Can i do an OTA update of 7.0.4 and once that is done, i am hoping that my data and everything remains intact and then take a backup in iTunes and then restore again to 7.0.4 using iTunes so that in future jailbreak.

WB2Colorado said:

Yes, exactly.

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Thanks for your help. Really appreciate it.