You need to place all the apps your removed back. There is no "backup partition" that holds a copy of the phone the way it came from the factory.
Restore all the apps then you can do a Factory Reset.
Factory resetting on one with missing apps (required apps) will cause more damage.
Motorola Droid - SnkBitten 2.2.6 - Froyo
Motorola Droid 3 w/root - Gingerbread
Motorola Droid 4 w/root - ICS
Samsung Galaxy Tab 10.1 - ICS
Logitech Google TV - Honeycomb
Motorola Xoom w/root - JB 4.1.2
ASUS Transformer - ICS
Viewsonic Gtablet - *beta JB*
Google Nexus 10 - JB 4.2