Joe,
The answers to your questions are:
Yes, you will still have a 1/2 cock but not a 1st notch (useless anyway, but no 'click').
Yes, the chambers will still line-up properly like they do now.
But the action will be stiff. The conversion trigger will have a bump on the back of it to increase the trigger spring pressure. Grinding it off will help a lot. Also you have more parts moving around so slicking them up or polishing will also help. There will be a groove on the right side of the hammer for the transfer bar to fit in which is kind of ugly when cocked.
The new parts that will be installed are retrofit parts made to work in a 3 screw gun and not the same or as sophisticated as the new model.
If you send it back to Ruger, call 1st and get a prepaid shipper and there will be no shipping cost to or from. Also strip out all the internal parts including the hammer, trigger and cylinder pin and keep those at home. There are reported cases where those did not come back with the gun. You can either keep them for the gun or sell them.