Given that the amp has worked perfectly for so many years with 5U4s I can't see that the swap will cause any problems, and they do come with the 5AR4 now. But forgive us if we pick apart your amp for a minute.

This is a pretty cool design, switchable SE/PP with adjustable feedback settings. The power supply follows some different rules, however. You can see the schematics here:
https://www.radiomuseum.org/r/manleylabs_sepp_300b.html5U4 full-wave bridge into 650uF!! I wouldn't even consider second-guessing Manley's designers, but it's interesting that they get away with that. The rectified DC is tapped off the rectifier filament supply center tap, with a hefty 100 ohm resistor before the caps, all of which, I assume, goes to protect the rectifiers from the effect of the large caps. Also, the B+ is not very high, and they don't appear to be running the 300Bs very hard, so the current demand on the rectifiers probably isn't excessive. It looks like a pretty conservative design.