Just wanted to post what I had already shared with Reyn earlier. Recording for posterity.
My experience has been with my Giant VT, but may apply to other bikes.
Small-small gearing, chain rubs on bottom of front derailleur cage, and FD is as low it can go
I have had this problem, but pretty much ignoring it, because I do not shift to small-small on rides (realistically, no one should, because of the angle stress put on the chain). It should be normal for the most part, because the line that is created from the small cog and the small ring is really low.
I am also assuming that you are measuring the clearance of the lower, outer edge of the front derailleur and the big ring teeth, and not the clearance of the derailleur in its shifter-engaged resting position over the big ring? The difference is almost a couple mm, which you can recover for your small ring.
Rubbing occurs on the inside of the rear derailleur cage when on the middle chainring and largest cog
First thing is make sure that the drive side crank is "pressed" up against the washer and the BB cup. Make sure you take out all the gap; in fact, you should not see the spindle on either side of the BB shell.
Next, put the chain on the middle of both front and rear gears. Does this draw a straight line?
On my VT, I had to move one of the spacers over from the drive- to the non-drive side. My BB shell is 68 mm, and according to the RF directions, I should have two spacers on the drive side, but that was actually causing some shifting issues for me (not really "ghost shifting," but essentially I could not get the gears to shift fast
I then noticed the angle created by the spacing (as well as the gap between the chainstay and crankarms not being equal on both sides).
Once I moved the spacer over, the gap was equal, the drive train angle was straight, and shifting was lightening fast.
You may have to do the same if you are exhibiting the same symptoms.
Long cage rear derailleur? Perhaps hub differences?
The rear derailleur cage should not really play in all this. But, you reminded me that there ARE hub differences!
I have two wheelsets that revealed to me that the cassette alignment is different. I found that my WTB LaserDiscs places my cassette a tad further INSIDE of the dish than my Mavic Crosslands.
I was switching wheels between my bike, and noticed that it was nearly 1/2 shift off when changing gears!
Hope this helps. I'm gonna be helping sungchang with his build tonight, and I'll see if I see anything interesting come out of it.