Well, at this stage it appears whatever was causing the bounding box size thing has sorted itself out.
Looking at the Outliner, it appears you have an interesting structure for this assembly. The shafts are just loose, ungrouped geometry and it looks like it would be a bit more challenging to adjust the positions of parts than needed.
I’m building a mobile base for my drill press, this is the leveling assembly, the shafts are 1/4-20 threaded rod through 1/4" holes. I’ve combined several designs I’ve come across over the years into something I thought I could use.
The rods were kind of an after thought, I applied a circle into the center of the leveler and just pulled it up. I still have issues with adjusting the position of components. This is the base: Drill press base.skp (723.7 KB)
As for centering things, the easiest way is just draw everything in place. You can also use Inferencing and if you set the component origin at the center of the component, you can quickly and easily insert the component by dragging it in from the Components window.
I downloaded the T-nut and knob from 3D warehouse, placing them was a real struggle. I made the foot as a separate project at 10 times actual size and added a small circle in the center (easy to do since it was on the blue origin) then scaled down and moved the origin to the center of the circle, it was still difficult to place.
I assume you used Follow Me to make the foot, and you did that in place? Then did you add the nut later?
I used my favorite method of starting the foot at it’s correct size and in place on the bottom of the shaft on the left end. I drew a profile for the foot and a circle for the Follow Me path on the shaft’s centerline. I also drew a hexagon for the nut while I was at it. I selected the profile, circle and the hexagon, made a component and then made a copy of the component. I scaled the copy up leaving the original in place and then edited it to run Follow Me and to make the nut. After I finished up the foot, I exited edit mode on the big copy and deleted it. When I went back to the original, it was complete and sitting where I left it. No need to scale back down and try to get the component in the right place.
I had the tee nut and knob from other projects I had drawn.