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You'll have to jailbreak, remove the mods, backup, and restore again
If anything does, then it's DFU because I definitely did that and set up as new phone and had no % indicator. Unless there is something different with 2G rather than 3G firmware.
The only time I had mods carry over myself was restoring from backups.
But if a % indicator is added as well or other such mods... they will not be removed.
When you do any firmware upgrade it resets all files to originals in the / directory but leaves a good portion of ~ or /var/mobile/ unaltered when you restore from your backup because this is where all your preferences are stored. Any jailbreak mod that changes files in this directory will generally stay if you restore.
That's why Cycorder videos, Preferences for Cydia apps, Cydia recent lists and so on stay between jailbreaks even if the apps are not still on the phone.
When I went to an Original firmware and set up as a new phone and then DFU'd and whent back to Jailbroken firmware and set up as new again, I had lost all my home directory including % indicator.
As indicated above, this may have to do with DFU then.