Welcome to TM, Kay!
I´m the very happy owner of a 4/4 Sport from July 2011 and I´m ok with the Ford gearbox. I also own a MX-5 (six speeder) and love it´s gearbox but I think in the very classic MOG the Ford gearbox is acceptable and indeed with some miles done it gets smoother.
As far as I know the first MX-5 gearbox fitted MOG in Germany was a narrow bodied Plus 4 in maroon red with black leather in January 2012 (ordered as a stock car by MORGAN Flaving in Düsseldorf).
One aesthetical point of view (negative at least for me) is the fact that the smaller (or lower mounted?) Madza gearbox leads to a gearshift that looks like "fallen" some centimeters (too much) into the hole of the centre console.
I´m not sure if in the meantime MORGAN shaped the console to a lower format to counterbalance that (which on the other hand could lead to a less comfortable support to brace your right leg on in a LHD car).
@Jays: Do you have any information about that point?
The gearshift in my Ford gearboxed 4/4 Sport stands "classically" upright in the centre console and I added a bespoke leather "casing" and changed to a nice polished "ball-knob". I love it!
Have a look at:
http://www.talkmorgan.com/ubbthreads.php/topics/140029/8But what is really shocking to me is the actual price list...

My 4/4 Sport in spring/summer 2011 was in the german price list with 42.400.- €, already
including the whole Sport specification (e.g. full Muirhead leather interior), the Sport pack (door handles + pockets), tonneau cover, mesh grille and photo documentation of the built.
Usually you´ll spend a lot of money to individualise your car (as I did extensively...

).
Buying a new 4/4 + adding the whole package of extras and goodies and finally having a bill of 65+ K€? Sorry, but IMHO that´s absolutely bonkers!
My tipp: If you´re not looking for a very special colour combination take your time and watch out for a well equipped preloved car with all the tweaks of a new MOG already sorted

and perhaps some nice upgrades already done.
However you´ll decide, go for a MOG - the conclusion will always be a fantastic car and a unique driving experience. You´ll love it (and not only vinyl...)
Kind regards from the Saarland to the north of Germany,
George