The bolts should not be doing that, they have their own skin modifier and are already weighted corectly, don't modify or delete their skin modifier, if you are using my JA skeleton of course.
If you have linked the bolts to your mesh already, DON'T!, you should not use reset xform when meshes or bolts have been linked together. Select your character model and hit unlink first.
To clarify on bones limit, "each VERTEX can only be deformed by 4 bones" not a limit in how many bones are in the modifier list. If you want to prevent this from happening, there's a section in the skin modifier where you can type-in the max influence (i think they set it to 20 by default...idiots!) so put 4 in there.
In that first screenshot i can see the bounding box around the mesh is all screwed up (the white bounding box) it looks right on the 2nd screenshot...so the xform has been fixed.