Answer: You should report 50080 (Percutaneous nephrostolithotomy or pyelostolithotomy, with or without dilation, endoscopy, lithotripsy, stenting, or basket extraction; up to 2 cm) or 50081 (... over 2 cm) depending on the size of the stone your urologist removed, which you don’t give in your question.
Then, you will report 50392 (Introduction of intracatheter or catheter into renal pelvis for drainage and/or injection, percutaneous) for the nephrostomy tube placement.
You should not report 50393 (Introduction of ureteral catheter or stent into ureter through renal pelvis for drainage and/or injection, percutaneous). Your urologist percutaneously inserted a stent antegrade through the kidney for drainage, and this antegrade placement of a stent is included in the procedure 50080 or 50081 and is not separately reportable or billable.
Reporting 50394 (Injection procedure for pyelography [as nephrostogram, pyelostogram, antegrade pyeloureterograms] through nephrostomy or pyelostomy tube, or indwelling ureteral catheter) is not appropriate unless your urologist performed a nephrostogram, which you do not mention in the above scenario.