Sounds like some data files may have been overwritten. You MAY end up having to do a factory reset to start over. That said, lets try resetting the Sense Launcher (rosie), which is what draws your homescreens and dock for you. Sounds like you can still get to SETTINGS (I hope), so SETTINGS-APPS click on ALL. Now, I have replaced my stock launcher so am not certain of the name, but you either want to find ROSIE or SENSE or SENSE LAUNCHER in the app list, select it and CLEAR DATA. Someone running stock launcher help us out here
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If this starts to cascade into another thing and another, is when the factory reset may be desired. If you do end up starting over, make sure NOT to restore anything Sense related. With the increase in OS level after the update, I am guessing that you are seeing an incompatibility between ICS and JB versions of sense data (or app) that you may have copied back to your phone.

If this starts to cascade into another thing and another, is when the factory reset may be desired. If you do end up starting over, make sure NOT to restore anything Sense related. With the increase in OS level after the update, I am guessing that you are seeing an incompatibility between ICS and JB versions of sense data (or app) that you may have copied back to your phone.