"I hate my saddle to handlebar drop, it's incredibly far for comfort, but a taller stem, even 140mm, feels weird as it cramps my arms even closer to my torso. I pretty much only ride on the flats now anyway, because of this problem."
OP; I have to assume that this comment is related to your current/old bike....or I hope so (otherwise you should discuss asap with your builder).
BTW/1; A 140mm stem is not taller, it is longer. The one shown on your old bike shows this. Your new frame design should be such that a stem in the middle of the range will fit and fit you (assuming you haven't stated a requirement for it to be otherwise).
BTW/2; The likely issue with your arms being cramped into you torso is probably caused by your existing bars being too narrow. "Wobbly" is also an effect felt by narrow bars. Suggest look for a pair of old Cinelli track bars as they came in crazy wide widths and are very open to let your chest expand, leading you to breath well and deep even when deep in the drops. But they are not for anyone riding upright much. The distance between my shoulder joints is 18 inches on center so I mostly rode 44cm width Cinelli track bars (my LBS owner recommended them upon measurement/fitting and had Mel Pinto import them for me; circa 1974-75). You might need a 48cm width, if that is even available. Your builder should be able to whip you up a set of bars to match your physique or source them if already being produced commericially(?). Bars are just one additional topic to cover with your builder.
BTW/3; Are you also considering longer cranks, heavier wheels, a bit bigger tires, longer CS's to clear your heels, etc.? Just a thought.
FWIW; If the pix at
http://i.imgur.com/UyQE0K6.jpg reflects the progress to date on your frame, then it looks very nice and well proportioned to your stated size. When you ride it for the first time, you will likely completely forget the old bike. Put that thing on Craigslist and take whatever you can get for it and don't look back.
Please post progress as you proceed. I suspect Gene is way ahead of you and will make you an awesome bike.
/K