I think you're onto something, but first... "It's Philosophy Time!"
When attempting to evaluate a potential "improvement" in a unit's performance, you need to run a "baseline test" on the unit, but you NEED to make sure the unit is operating as well as it can be. (Of course, one could argue that a *true* "baseline test" would include running a test prior to alignment, but we have some "prior knowledge" about the FM-3's alignment.)
Throughout the entire Monaural section of the tuner, adjustments are fairly broad. (It is important to be as accurate as possible with the Discriminator alignment, but otherwise, things are pretty simple.)
When you get to the multiplex board, the adjustment to T-71 and T-72 is broad and well-pronounced. T-73 is a bit of a bear. EXTREMELY small movement of the slugs can make a BIG difference in the Stereo Separation and noise rejection.
So, before you go any further, I would STRONGLY recommend doing an alignment of the Multiplex board. I think you will find the separation will improve - even with the strip antenna.
As for your research, I think you are DEFINITELY on the right track. The earlier FM-3 that I modified for 50 microsecond response didn't seem to suffer from the same issues. Sure, it was "bright" when listening to US stations' 75 microsecond pre-emphasis, but it was no more pronounced than listening to a dolby B encoded tape with the dolby decoder off. (That's probably the closest I can "describe" a sound quality in print.)
By the way, I wouldn't bother aligning the rest of the tuner at this point, but if your Multiplex section is WAAYYY off, I'd consider doing at least a Discriminator alignment before aligning the Multiplex board.
Either way, it *does* appear that the 100 pF capacitor should *probably* be reduced to 68 pF for proper performance. Next time I do an FM-3, I'll try to do a comparison, but in theory, it looks like you're right on this.
I LOVE to learn!