Another option that I have only thought through but not sketched out yet (I have no CAD software - so bar napkins are my usual level of sophistication for tech drawings) is to put the stock shifter on the trans wherever it goes. Then build a median 'shifter relay' directly forward (i.e. straight forward from the 3-4 shift line) that is a rod with the same height as the stock shifter rod and the same diameter - the pivot for this forward displaced 'relay' is in the same exact horizontal plane as the stock shifter. Then build a third device, we'll call it a 'proxy shifter' with the pivot in the same plane as the other two pivots, and the same rod length/diamter as the other two, this one located 90 degrees off of the axis of the stock shifter to the 'shifter relay'.
Now you have three identical linkages (not hooked to each other yet, that comes next) that all have the same height/diameter lever and pivot on the same horizontal plane. Stock one is where ever it has to be, relay is directly in front of the stock one, and proxy shifter is directly to the side of the relay (all assuming your trans is too far back but basically any displacement can be addressed by two right angles as long as you can keep everything in the same plane).
Now go find a heim joint that fits the rods (as far up as possible to allow for all the errors in fabrication, and you actually want to buy all the rods / modify them to fit a size you can get heim joints for in planning - but you knew that) and buy four of them. You'll cut one of them and weld part of it to make a right angle fitting for the relay rod with it (you end up with a stock heim joint, with an extra female thread portion 90 degress offset, and in the same horizontal plane as the original one). Then you'll mount that to the relay rod at height x up from pivot, mount one of the unmodified ones to the stock shifter x up from pivot, then the last unmodified one to the shifter proxy at height x up from pivot. Then use tie rods or something similarly crappy to tie them together (start with the lengths between the pivots, and I imagine you'll end up fiddling with it to get it to make it shift). You'll need bracing between the two right angle tie rods - probably a lot of it, and reverse may not be manageable with this goofy linkage.
Caveat: I haven't built this yet, so if it doesn't work for some glaringly obvious (or otherwise)reasons, you should have known better than to listen to some guy on the internet. If it does work, I'd appreciate pictures of it completed...
Good luck.