Thanks for the replies, guys. I may have posted a bit prematurely on this, as I think we made a breakthrough last night after I posted, but we won't know until a part or two comes in. Here's what I think is going on, apologies in advance for the length.
I went back to another post I put up on this topic on a different forum, and one of the replies I got there indicated that the flasher resistor rating relates inversely to the number of flashers running on that line. The higher the resistance, the fewer flashers on the line.
So that equates to:
1 flasher on the resistor: 11 ohm
2 flashers on the resistor: 5.6 ohm
3 flashers on the resistor: 4 ohm
4 flashers on the resistor: 3 ohm
The manual does, indeed, say 3 ohm 5 watt resistors for the flashers. But the manual has a lot of specs that are from the prototype machine, including the original diverter arm assembly and a bunch of extra flashers behind the translite (which were removed on later machines - mine does not have them). These backbox flashers were also run off the R1-R9 resistors.
So, with those extra flashers, it makes sense that the manual would have those resistors at 3 ohms since they'd be running up to four flashers at a time (some on the playfield, some in the backbox). I appear to have the same setup installed as nifti, with several 11 ohm resistors running single flashers, and then a few 3, 4 and 5.6 ohm resistors.
And to correct an error in my original post, I have three flashers out: two "domed" flashers and the one that's just below the Atomic Whip coil. Those appear to be on the the Flash 2 circuit, and R2 is a 4 ohm resistor (as Nifti's picture above confirms). Tested it, and sure enough it's closed. I had tested it earlier and it read 11.2 ohms, but I couldn't read the rating printed on that particular resistor, and since there were several 11 ohm resistors mixed in, I assumed it could easily be another 11 ohm resistor. Once we figured that three flashers on a line would use a 4 ohm resistor, it made sense. Reading 11.2 on a 4 ohm resistor six months ago means that thing hasn't been working for a while, and last night R2 was completely closed.
Time to order a few resistors (a 4 ohm for the R2 and other backups). I'm not 100 percent sure this will solve the issue, but I'm very hopeful.