Indeed. I'll chime in with the reassurance that there's little "wrong" with the modelling of 'physical' objects.
It tends to be a bit heavy weighted later on. But refactor it a bit at a time. For instance, everything you describe sounds ok. But I don't have to work with it, so it's tough to figure out where the sticking points are. All I can really advise is to pay very close attention to "I wish I could just...." thoughts. Optimistically write it top-down as far as you can, then the design difficulties will emerge in a pretty clear way.
Either way, sounds like your thinking on the right lines.
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