ok, just read back through this whole thread...armen, i have never heard of such problems with dropouts! maybe i have been out of the MD game for too long, but it's really only been 1.5 yrs since i was strictly taping on MD, and only a patcher then...i don't recall any dropouts (at least i can't remember right now) from moving the deck in the field, of course i only tape taper friendly bands and usually have a place on the ground to stash the deck, so movement is minimal when checking levels or time remaining.
i only did md transfers on this weird japanese sony md station...it has a removeable deck similar in size to the larger md decks (not the squarish ones) and docks in a little station, about the size of a cable box (on top of your tv) but shaped very oddly....i'll have to take a pic of it. i think the model is mzr4st. anyways it has an optical out and i went into my soundblaster live 5.1 with digi/opti i/o module (yeah i used sb live but it frikkin worked fine at the time and was relatively cheap!) and, as i said before, i don't recall EVER having any dropouts. maybe because it was another "portable" type machine i was going out of and not a home deck.
anyways, just wanted to drop my .02 in the bucket.
that does sound like a LENGTHY LENGTHY process for you, but your supreme dedication to quality fixing those dropouts earns you a +T and mucho respect. that's more patience than most have.