The 5ar4 is an indirectly heated rectifier tube which allows the cathode and anode to be very close together for minimal voltage drop. The NOS 5y3 is a directly heated rectifier which has a substantial voltage drop. I'd expect to see 20-40 less volts with the NOS 5y3, maybe more. You can always change the cathode resistor to a slightly higher value when using the 5ar4 and allow the tubes to idle a little cooler but the tone of the output tubes changes slightly as plate voltage and current change.
FWIW, the modern Russian made Sovtek 5y3 is in truth a re-labeled Russian indirectly heated rectifier and will have far less voltage drop than a true 5y3. This has been a problem for many a builder but can be taken advantage of if you want to increase plate voltage in a 5y3 equipped amp.