I worked with some really bright college kids that had the same problem.
They were using a Ford Aspire 1.3 with the single rail 5 speed and were trying and contemplating everything.......hydraulic, robotic, chains, cables, linkages out the wazzu!
While I really liked many of their designs (paddle shifters are cool...but expensive) one of the goals was cost and simplicity.
My main contribution wes when I had them use the stock shifter...just turn it around to shift towards the back. Smart people are sometimes too smart.
This gave them lined up linkage with an engine in the way.
When I left them they were looking at one cable and 2 cable designs to translate the motion around the lump.
The real shocker was when I came back 3 days later.
While the 2 cable version worked flawlessly, some bright boy had taken advantage of clearances, machining and such to run a 1/2 rod between the oil pan and bellhousing just under the rear main to a very clever lever that translated both rotational and longitudinal movement.
This was simple and within my meager fabrication capabilities, but these guys have access to more equipment than I could imagine.
As an offhand remark I asked if it was possible to machine the shift rail out the front of the tranaxle.
Looking at the blow-up diagram, it appeared that it was very possible.
I know these guys are capable as their current setup has the clutch/flywheel replaced with an hand built electric motor/generator/starter and a 2 cylinder veggie oil motor hybrid.....yes it's cool.
They also estimated about $200,000 in costs over 2 years.
I haven't looked in over a year, dang thing may fly by now.
Bruce