Fitting the oversize bolt: the cylinder slots are about 0.105" wide, and the bolt window in the frame was originally about 0.1055" wide. The logical thing would be to stone the oversize 0.107" bolt down to about 0.105" for a snug fit.
But .... I had a clever idea.

Since the cylinder timing was off by a good 0.003", why not shift the timing by a combination of filing the window 0.001" or 0.002" wider on one side so that the 0.107" oversize bolt could fit, and then file the top of the bolt on one side to 0.105"? In theory that would shift the timing over about 0.003" while providing a snug fit at all points.
So I tried it, but when I checked the alignment, it was worse, not better. I figured I must have screwed something up so I started over, making a homemade bolt from barstock. Let me tell you it was a son of a gun to make that homemade bolt and in the end it would not cycle properly because its hole was located a few thousandths off.

Nonetheless this photo of the homemade bolt illustrates how I was attempting to shift the timing by making the top of the bolt offset relative to the bottom of the bolt.

Since the homemade bolt wouldn't cycle, I tried again with the Power Custom bolt, welding it up oversize, then grinding it down. But no joy , alignment was still worse. All I can figure is that my original alignment measurements with the factory bolt were optimistic because there was enough wiggle in the cylinder timing to allow the gage pin to self-align its way into the throat.
Here is the alignment with the oversize bolt
#1 -- 0.354" pin
#2 -- 0.352" pin
#3 -- 0.353" - 0.354" pin
#4 -- 0.353" pin
#5 -- 0.352" - 0.353" pin
#6 -- 0.353" pin
average -- 0.353" pin, or about 0.0045" misalignment.
Even thought the oversize bolt eliminates the wiggle in the cylinder timing, I could still wiggle the undersize gage pins in the 0.358" stub, so the actual misalignment is probably more than the measured 0.0045".

I suspect the actual misalignment is closer to 0.006".

That sucks, but it's not unusual for a mass produced revolver (perhaps CNC technology has improved tolerances on recent production revolvers, but CNC was not being used when this Dirty Harry era frame was manufactured).
The fitted oversize bolt will be absolutely necessary when I get around to making a line-indexed cylinder, but in the meantime, would it be better if I went back to the sloppy factory bolt? Perhaps, bearing in mind that the hand will take up most of the slack in the cylinder timing, and it so happens that the hand will be pushing the cylinder in the direction that it needs to go.
Retesting with the factory bolt:
#1 -- 0.353" pin
#2 -- 0.353"
#3 -- 0.3535"
#4 -- 0.354"
#5 -- 0.353"
#6 -- 0.3525"
average -- 0.3532", or about 0.0043" misalignment.
That's worse than my original measurement on Oct 21. The difference is due to how much I wiggle the pins. If I wiggle the pins aggressively enough, I can get a 0.354" or even 0.355" pin to go, but that's probably "cheating." Wiggling the pin effectively pries the cylinder into alignment.
Does wiggle in the cylinder timing allow a bullet to self-align in the forcing cone? There are several problems with that theory. 1) the front band of the bullet will still slam into the forcing cone off center. The best that can be hoped for is that the cylinder will then self-align for the remainder of the bullet 2) inertia may prevent the cylinder from moving quickly enough to self-align and 3) the hand pushing on the cylinder ratchet may take up most of the slack in the cylinder timing, anyway.
Well, my clever idea to shift the cylinder timing with the stepped bolt did not work.

I'll set the oversize bolt aside for the time being and use the factory bolt with the factory cylinder. I will have to cut the forcing cone to allow for at least 0.006" mis-alignment -- in other words, the entrance to the forcing cone will have to be at least 0.370".

Accuracy will probably be disappointing due to the misalignment and the oversize forcing cone, but that's a fact of life with mass produced revolvers. Buying a mass-produced revolver is a roll of the dice -- sometimes you get lucky, but I've been unlucky with revolvers more often than not. That's why people pay big bucks for FA's or for custom line-bored cylinders.