Yep threaded all the way through. If you need it, the last kit I bought was from Mikes Bikes, part #A095A for 2" downtube. Drill out the rivets and remove the boss and residual rivet pieces from the downtube (through the headset or BB).

I would go ahead regrease everything but that's just me.

A Nitto Technomic stem should get you the height you need, try Tree Fort Bikes for that.. I just received a new one from them along with a set of Noodle bars for my Trek project.

You'll need to oversize the P-clamps and bend them a little to fit around the seat stays since they are oval and oversized for the rear rack.

Enjoy it.