To fix the bounding box - open the object in SimPE. Click the GMDC and on the Model tab you'll see "clear" - click that and it will clear the bounding box. Then go to the Groups tab, click on the subset you want included in the bounding box then click "add to bounding mesh". (You'll probably want to do this to each subset EXCEPT shadows - unless you have a good reason you want to limit where you can grab or click on an object in game.) Commit and save when done.

To fix thumbnails that CTRL+Clicking in game doesn't fix: Click the CRES then the Blocklist. (Not the CRES heirarchy.) Look for "Thumbnail extension" in the dropdown and click on it. If there is an entry in the Items box, click on it and then delete. Commit and save. The game should then have the correct thumbnail the next time you load your game. (If your object is bigger or smaller than the object you cloned, the thumbnail will usually be wrong and regenerating it in game won't fix it. This *will* fix it IF there is anything in the Items box for you to delete.

Your footprint edit: I'm not sure exactly what you did. I haven't run into any Maxis objects that are larger than 1 tile and didn't have multiple OBJDs/etc to edit. (Custom objects? Yes. I've plenty of decorative objects that are larger than 1 tile and are just centered on it OR take up just 1 of the tiles. Annoying and I should fix those objects some day!)