Why I now do all my rebuilds/recaps of vintage gear in stages.
I am glad you are doing the rebuild incrementally, instead of doing it all at once, like you said at first. I have found that if you (like me) are not a professional, doing too much at once is always problematic. The more parts you upgrade at once, the more things can go wrong, and in my case something is always amiss. I now concentrate on one specific area (like main power caps, power supply caps, preamp board caps, protection/muting circuit, poly film caps, etc, then play the amp for a day or two to listen, and check voltages, bias, etc again.
This way when something goes wrong and the amp shuts down or whatever, I can narrow down the problem (me) to the specific area I just worked on. Since I don't have an o-scope, variac, etc, this keeps me from getting stuck.
Also, I enjoy checking out the improvement of doing a specific mod at a time, or a specific brand of part at a time, so I can gain some knowledge fo ther next build. Usually while recapping, other issues crop up anyway, and/ or I up my mod budget as I always do, and I end up ordering additional parts and waiting again!
I also have a theory, completely unproven, that changing out like all 100 electrolytics in a big receiver at once can cause breakdowns, burn transistors, relays, resistors etc., by itself, since turning on tons of brand new caps at once can only totally stress out the amp.
I suspect that while new caps are forming and breaking in, they emit lots of leakage, surges of DC, noise, or whatever. I base this on the fact that leakage current of electrolytics goes down after the first five minutes or so of operation. When I change to big main output caps/ rectifiers, that is all I do, then I leave the unit on for a few days, like a surgery patient in a recovery room.
Also, for safety reasons and to minimize mega breakdowns, I like to upgrade roughly in this order, -- cleaning and deoxit, smaller Power supply caps, protection circuit/muting, main Power supply caps, PS diodes and power resistors, amp lytic caps, preamp lytic caps, film and bypass caps, resistors, etc.
There is nothing worse than adding tons of super expensive, premium film or oil caps, 6 nines copper wiring, jacks and IEC; WBT speaker posts; stacked film resistors, Black Gates, Mundorf, teflon caps, bypasses everywhere, etc, etc . FIRST (before the PS and protection circuits), then the marginal power supply blows out totally due to some tiny error, and your dream amp is now a boat anchor with $500 of superstar parts, mostly unsalvageable-- soldered into it with the leads clipped off. Don't ask me how I know this......(sniff)