Help with hum

Been there.Save yourself some grief and borrow or steal another pre amp,plug it in the system and if the hum disappears you will have identified or eliminated the pre amp as the source.

Has it always hummed?

I think the manufacturers specs for hum on your pre are -88db below full power. Whether or not this results in audible hum on most systems I can't answer, what I do know is that there is audible hum with either of two tube phono pre's that I've owned and with my current tubed pre. I've come to just except it as part of the cost of going the tubed route.
An option, assuming that you have plenty of gain in your system, would be to call manley and ask them about reducing the gain on your power amp, this is usually an easy thing to do but I'm not up on the manley's. If you have a friend who is handy with electrical stuff they could make a very inexpensive couple of voltage dividers for you to play with as a way of determining whether reducing system gain seems like an improvement. Tweaking down the gain on your power amp obvisously won't eliminate the hum but maybe take it to a point you are more ok with. Good luck.

Sounds like another case for balanced operation.

Removing the preamp stops the hum. All of your circuit design issues regarding grounding and loops are not to be ignored.
However as an owner of a couple of tube pres including a Cary Low end brand. I can tell you that a bad tube can cause a number of different noise issues. I always took the stock 6SN7s out and rolled in a wide variety of old stock. Man oh man I couldn't believe how many fine testing for transconductance when put into a preamp how noisy and bad tubes reared their ugly character.
Thus my question Have you experimented with the tubes? How many hours do you think you have on your preamps tubes?
Obviously you know what I am going to suggest you do. Roll some different well tested tubes into the pre. I know the other sugestions seem more plausible at first glance, but so far grounded has not changed you problem