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The goods have to be shipped from somewhere to somewhere. How hard would it be for the feds to find the origin of the packages?

Its tough separating the wheat from the chaff. Presumably, Silk Road merchants aren't the first to ship drugs: it's pretty tough to detect without slowing everything down.

You can't shut down a Tor hidden service without compromising or shutting down the entire Tor network. Same deal with Bitcoins.

I think maybe the endpoints can be targeted where bitcoin is traded into dollar. But I have a limited understanding.

It's simple. I will monitor your networks and if I see somthing that looks like TOR(omg) I send my police buddys to shoot you in the face.

Exactly. It would be exceedingly difficult to locate the silk road server, but trivially easy to find someone who was going to it

No it wouldn't. You can determine if someone is running Tor, but not which sites they are visiting with it. That's sort of the whole point.