1) Why would you add up the tubes draw to figure the fuse rating? Wouldn't it be easier to just set the fuse for the PT winding's rating? For instance, the filament winding on this PT is 6A. Instead of fooling around, why not just fuse it for 6A? Likewise, although I use a 5AR4, the recto winding is rated at 3A. Same question.
It's a matter of one's theoretical approach. In this case, it would work fine. You'd like these protective items to protect BEFORE the thing they are protecting overheats. You want the fuses to blow at a clearly "over" condition, not necessarily at a "maximum allowable" condition. Heater fuses are somewhat of a grey area. When cold, heaters can and typically DO use a tremendous amount of current for a very short time.
Suppose your tranny was rated 50 amps heater current. Would you advocate selecting a 50 amp heater fuse? I think not. What about 10 amps? By the time your Deluxe Reverb tube-complement is using 10 amps on anything but a momentary basis, something is big time wrong.
2) Should the F2 and F3 be equal?
Yes.
The article never mentions F3 but it would make sense that it would be the same as F2.
Yes.
3) The diagram of fusing in mod #2 shows a capacitor before the B+ fuse. What does it do, why is it there, and what should it be?
A power supply charging the biggest of the big caps for the first time, on the first charge cycle, could produce an inrush current well in excess of normal operating conditions. If that first cap were located after the fuse, the fuse would have to be rated at high amps to avoid blowing the fuse all the time on startup/inrush current. If it were then that big, then it wouldn't have much protective function in normal operation. This is the general challenge on all of these things: To select a fuse rating that doesn't blow on first turn-on/inrush current, yet still protects, and protects BEFORE smoke.