If you wanted to reduce travel after activation, could you drop a small ball into the plunger shaft? A soft ball would also cushion the bottoming out. I find the standard 3mm travel, 1.5 mm before and 1.5mm after activation pretty good.
FYI - The switches you're testing are new so are probably as scratchy as they ever will be.
I wonder if the ideal process would be to use them unlubed for a while to wear them in, then lube them?
Do you think it's necessary to disassemble the switches to lube? I ask for two reasons. First, as you know the switches are quite small and fragile, if opening can be avoided it would be a plus. Second, most of the contact points can at least be partially reached externally.
I don't notice binding if I strike the corners of the keycaps as much as when the strike isn't vertical. I agree however that the round top ML caps would probably be helpful.
I think I'm good with the .7" horizontal spacing too. Once you get use to it, the advantage of having the keys closer is a definite positive. Do you think there's merit in the vertical spacing being a bit tighter? My earlier testing found .65" to be ideal for my hands but I think I limited it to that because I couldn't fit a tighter spacing with either the MX or the Alps style switches. A future board may try a .6" to .65". The only spot where I would have liked a greater vertical spacing is between the thumb keys. If I moved the upper thumb rows away from the alpha's, there would be room to raise them .1 to 1.5" which I think would feel less cramped. Part of the problem is the way I contoured the upper thumb keys; they cramp the lower row a bit. Reshaping them may solve the problem.
Thanks for the results of your preliminary testing. 
Yes, you could definitely use a tiny ball or a tiny disk of punched metal/rubber beneath the plunger to reduce travel. It's important to note that reducing travel after activation is far less for comfort, and more to increase the ability for rapid double taps. It's virtually impossible to make use of the minuscule tactile bump for double taps, which quite frankly only gets in the way. Ideally pro gamers want (or should want, in my theory) as small a travel after activation as possible specifically so there is also minimal travel required to reset the switch on the upstroke. I think this is why gamers tend to favor red cherry switches with O-rings under the keycaps - they're actually trying to mimic the bottom-out activation of rubber domes by eliminating over travel.
I would agree that ideally you'd want to wear them in unlubed, then lube them later if you want maximum smoothness - or just never lube. The lube tests I did today on new ML switches were not very successful, making me think that I had imagined any improvement from before.
Perimeter of switch lubed without taking apart = felt little to no difference in scratchiness, same potential for binding
Perimeter of switch and plunger lubed = still felt little to no different in scratchiness, tiny bit less bindability on corner presses
Removing the metal contact completely = felt less scratchy, but switch obviously can't work. I just did this to test a theory that much of that feeling comes from the triangular plastic sliders rubbing on the metal contact. Putting any lube on the contacts sounds like a horrible idea though.
So I'd recommend just keeping the switches dry. They really only bind if you are purposefully trying to get them to, pressing on a corner in a way to tilt the key as much as possible before depressing.
As for reducing vertical spacing further, yes, I do see the potential provided it is compatible with your anatomy, however, that may be contingent on building in a step, or a pseudo step provided by angled keycaps.
For the thumbs, you're talking to someone who only uses a single thumb row, so I'd support keeping the thumb rows spaced quite far apart vertically and in elevation, but I think this is where anatomy plays perhaps the largest part.
Lastly, as for Pulp Fiction, it's one of my favorites, and was indeed the source for my selected numbers. It's probably about as opposite from Lady and the Tramp as you can get, though, so it just depends on if you are in the mood. I haven't given much of Tarantino's newer stuff a chance, because they all look so dumbed down for mass consumption, but Pulp Fiction is definitely an intelligent and hilarious movie if you can get past the comical violence.
