An isolation transformer is rarely needed for amp repair. I would use it for the littel transformerless hot chassis things that come out of record players. Your average guitar amp has a power transformer, and that offers isolation right there. Coming out of the wall, the 120vAC has one side connected to ground. This has potential for problems in some circuits and some procedures. An isolation transformer provides the 120VAC for a circuit to run on, but it isolates it from ground.
As to tubes or no tubes, it all depends on what you are trying to accomplish with your variac. No offense, but your question is sorta like which way should I turn my screwdriver.
If I want to see if there is a short on the mains, I don't care if the tubes are there. If I want to see if a rube is breaking down, they have to be there. If I want to see if the B+ supply is blowing fuses, then I'd leave the tubes out.
Education is what you're left with after you have forgotten what you have learned.
Oh. I never bother. In 50+ years of soldering I have never had a new electrolytic cap fail for lack of "forming." However, it certainly cannot hurt.
If that is what you want to do, then leave the tubes out. No point in having them in there getting hot, and potentially being mis-biased during the procedure. I would want tubes in the amp while working on or assessing the performance of the amp. But cap forming has nothing to do with how the amp works, it is an attempt to make sure the caps work, nothing more. So for that, you are just using the whole amp as a DC power supply, and the variac to make it a variable supply. Don't need tubes for that.
If the amp uses a tube rectifier, it won't be happy trying to make DC at reduced voltages, so mount a couple diodes in place of the recto tube in that case.
Education is what you're left with after you have forgotten what you have learned.
If you start at 33% wall AC (40VAC in US, 80VAC in EU?) your tube rectifier will work just fine, if you monitor voltages as you bring the voltage up in increments (10%?) you can make any adjustments as you go. You will probably still need to fine tune bias on a fixed bias amp after switching to wall AC, depending how accurate the dial on your variac is.
The advantage to having the tubes in place is that you can sometimes hear early on if things are wrong, before full voltage is applied.
Is there a preferred rate of increment of the AC from a variac when forming caps? Which steps (10%? 30%? or..?) should I apply and at which speed of change?
Whatever the answer is... should I apply the same method when I power up an old amp to check if it works, or may I simply increase gradually (but not too slowly?) the AC voltage?
Furthermore:
should I start with 33% mains AC like per MWJB above, or am I better off using a plug-in ss rectifer (that I have at home)?
Sorry, I was referring to bringing the amp up slowly to form the caps.
I'll form the dielectric on new caps with a variable high voltage supply. I use an old Heathkit IP-32 I rebuilt and upgraded. It works great for doing a whole batch at once through a high value isolating resistor on each. The Sovtek 5881 variants make great pass regulators in those supplies...they sure don't make great audio amp tubes tho.
If there's only 1 or 2 I'll just use my Sencore LC-77 to tell me when they're ready for action.
Its not really a big issue, new production caps (as long as they're fresh) should be ready to go out of the box. Trouble is, you don't know how long they've been sitting on the shelf before you got them. Better safe....
The farmer takes a wife, the barber takes a pole....
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