Thanks for the most recent information, that helps.
>> I plugged the PF in again (probably shouldn't have but...). The tubes lit up; ...
Just to confirm, the two 12AU7 tubes had an orage glow from the cathodes, and the 0D3 in the center had a purple glow on the inside of the cylindrical plate, right?
I don't see anything in the thread that indicates the smoke and blown fuse problem have been identified and fixed. That does concern me. Right now I only have two theories; one of them is that the 47uF/450v capacitor in the B+ supply may have been swapped with one of the 220uF/250v caps. They look the same, and this has happened before, so even if teh orientation of the caps is right, make sure they are the right caps as well.
>> transformer terminals measurements which were way off:
>> 4, 5 are 64 VAC (should be 3.3)
A high voltage is reasonable if your meter reads some kind of AC+DC on the AC scale. However this looks some 30-40% higher than I would expect.
>> 6 is 489 VAC (should be 165.5)
>> 7 is 487 VAC (should be 0)
>> 9 is 489 VAC (should be 165.5)
>> 10 is 221 VDC (should be 0)
Apparently 7 is not really connected to 10, since they give very different readings. The second theory, though unlikely, is kind of dangerous, so I think you should back up here in order to go one step at a time. First, unsolder and detach all the wires from power transformer terminals 6,7,9, and 10. You may need some solder wick or a solder-sucker to do this easily, those are inexpensive tools that will serve you well in the future anyhow. Then measure the resistance from 6 to 7; it should be about 85 ohms. Repeat on 9 to 10; it should also be 85 ohms. Then measure from 6 to 9; it should be infinite. If these all measure correctly then the transformer wires are not internally damaged and you can proceed. Now connect 6 to 9 and 7 to 10 as in the manual; but go ahead and solder 9 and 10. Now measure the resistance from 6 to 7, and from 9 to 10 - they should both be around 47 ohms. If not then the solder connection is bad - that's why I said to actually solder all connections here. Once these are correct, you can re-attach the twisted pair that goes to the power supply, again being careful that the correct wire goes to each terminal (9 and 10). You may need to wick or suck away some of the solder to get the new wires into their terminals.
Other than that, these readings are not unreasonable given the way some meters work.
>> All the other checks were fine.
If that is so, then the problems due to different meters are not really problems. Fix that connection between 7 and 10, and you will be good to go. Pay special attention to T21 and T22 - if the 0D3 is working correctly these will be quite close to the manual, a few percent a the most.
Hopefully somewhere along this path you will have found and fixed something that caused the blown fuse in the first place. But let it sit on the work bench running for long enough to see if the new fuse will blow (it is a 1-A fast blow, right? You checked?), or if there is any smoke, just to be sure. I would then recommend installing it in the base, right side up, and operating it for at least an hour, again on the work bench where a blown capacitor leaking gooey stuff won't ruin any furniture. Do this while you are present so you can keep an eye on it and spot any emerging smoke - don't walk away and leave it until you have proven it can be left on without problems. Re-inspect for bulging ends on electrolytic caps and anything else fishy. If there are no problems, you have pretty much finished fixing the problem.