power up and shut down

I would leave the pre-amp on all the time unless advised otherwise by the manufacturer. Otherwise it is best to always have preamp on and stabalized to ensure solid state amp sees no DC during warmup. I still prefer to leave my tubed preamps on all the time.

At the risk of committing heresy, I think that sometimes too much is made of the switching sequence issue. If you decide not to leave your preamp on all the time because of tube wear, then simply use your ears - and take off the speaker grilles to use your eyes as well - and hear/see exactly what effect switching off the preamp with the amp turned on has on the speakers. If it doesn't sound/look too nasty, then it probably isn't in reality bad for the speakers. This will depend on the preamp's switch itself, and also the amp's input sensitivity/gain as well as the speaker's sensitivity. Unless the transient produced is scary bad, I just wouldn't worry about this (even if it is an annoying sensation). However, if you're worried about even testing this result, then don't!

Thanks for the suggestions..
I've tried switching off the preamp while the Aleph 3 is on. Power up = annoying little 'buzz' (about 5-10 seconds) while the tubes 'engage'..(Can DC current hurt the amp?). Power down = two (always two) tiny pops and done.
I've been searching desperately for the source of 'hum' in my system and this compounds my frustration... I've tried cheater plugs on the components, cheater plugs on the 'surge protector', tidying up the interconnects and power cords, sacrificing a goat...

Although I don't know why you seem to suspect that DC is being passed to your amp, if the amp hasn't blown a fuse or shut down and is still working OK, then it presumably isn't being harmed by anything. As for the hum, you'll have to go through an elimination process to determine where it originates. For instance, try removing the preamp from the circuit by plugging your sources directly to the amplifier (no need to actually play them); if the hum persists with all sources, try listening to the amp with its inputs disconnected, etc. until you identify the guitly party. (And speaking of parties, I would suggest a nice Jamaican jerk sauce preparation for that late goat of yours...)

Have you tried a different brand interconnect?