although sibilants were an issue with my Dual 606/2M Red combo, and generally the high end could be a bit grating in my lively room.
The sibilance issues with your TT/cart is most likely totally unrelated to the amplifier, and may just be a matter of "tweaking" the cart alignment, or changing to a different cart/stylus that may be more compatible with your TT/arm combo.
My options appear to be: 1) Repair the Yamaha 2) run the 3140 as a preamp and upgrade to a more robust power amp in hopes of regaining the lost heft delivered by the Yamaha 3) start over and buy a new integrated. I'm leaning towards option 2, but am looking for advice on whether the difference in sound might plausibly be attributed to the disparity in power between the 3140's 40 watts and the Yamaha's 120 watts. Or do the units just sound fundamentally different and no addition of power will change the 3140's preamp sound signature?
I doubt the power differential between the two amps is a major factor in their "sonic signature" with your speakers. Although I am one of those in the camp of "you can never have too much power", in reality, most people rarely listen at levels requiring more than a few watts.
In reality, the difference is as you stated--the units just sound fundamentally different. In a perfect world, all an amplifier (just the amp section) should do is take the small signal it is fed and amplify it to a useable output signal for driving speakers--we all know this is not entirely true, but (in general) the amplifier section has little to do with the overall "sonic signature". Sources and preamplifier stages have the greatest impact on the "sonic signature"--some manufacturers even "tune/design" their preamplifier stages to a "house sound" that is fairly "unique/identifiable" to their brand.
Unless you are really committed to a vintage system, I would recommend option 3 above. Go check out the new Yamaha integrateds--I don't know what your budget is, but the A-S501 should probably fit the bill for your needs (and then some). They can be had for ~$500-550 from a lot of different vendors (most of which have very generous/hassle-free return policies), are available in either silver or black, still have a rather "vintage" look, a phono stage, as well as a built-in DAC to accomodate modern digital sources. At 85 wpc, it should be "healthy" enough for your speakers (its "bigger brother" the A-S701 is 100 wpc, but the price jumps to ~$800--so I don't consider that as much of a bargain).
If you go that route, you can sell the NAD to recoup some of the costs, and keep your current Yamaha as a "winter project"--it would be cool to be able to do an A/B comparison of the old Yammie vs the new one.