Was that you who moved everything over, after you found it was off center....or was that someone else, with a whole different problem....??? Hhmm, no, it looks like that was you.
Everything should be listed in Objects dialog.
There are a couple of settings you might want to look at. Inkscape Preferences > Tools > Bounding Box to use. You might want to choose Geometric Bounding Box. This will eliminate things like the stroke width from being added into an object's dimensions.
Also you might want to look at a setting which will scale the stroke width by the same proportion that you scale an object. It's on the Selection tool control bar, the first of 4 similar-looking buttons on the right end of the control bar. Looks like this:
. It just depends on your goals as to how you set that. But having it set differently than you expect or intend could help contribute to mis-sized objects or drawing.
Would you be able to share the SVG file with us? It sounds like too much might be happening for us to be able to guess what the problem might be.
