Just a couple thoughts. Your system is the "old" R12, I'd guess. The "new" stuff is R134. I've got R134 Vintage Air systems on one old OT classic, and a Classic Air R134 on my 55 'bird. I've got R12 on on OT '92. The R12 is hard to come by, very expensive, and will probably become unavailable.
All the new, small, aftermarket compressors, like the Sanden commonly used, are R134 . So, you're going to have to match the 134 and it's compressor to the R12 evap, condenser, dryer, etc. Plus the drop in efficiency from R12 to R134. Then convert the seals, hoses and o rings to R134 compatible. Not impossible for any good engineer who knows the specs.
I'd start with Vintage Air, to see if they can help. The system I have from them works like modern cars, and I have several friends with the same experience.
I've got a classic air "perfect fit" system on my 55 bird. It's ok, but not as good as the Vintage Air. But they do OEM and classic restorations. I'd call them next and ask.
http://www.classicautoair.com
Probably the best choice is to convert/modify the OEM to R134, and live with the big unit. What ever you do, don't modify anything beyond restoration, or throw anything away. That OEM system is priceless to guys looking to restore an optioned car. Which you've already got.