How long should one be on bed rest and obstain from intimate activity after a nephrostomy tube removal, and a percutaneous stone removal?

48 hrs and pain free. Recovery after tube removal should be fast. Wait couple of days and resume activity provided you are pain free and have no obvious blood in your urine. Advise partner that you will stop if activity causes pain.
Depends. This should really be answered by your urologist who knows the details of your case.