Recently (finally!!) completed the gen3 swap.  
 
One issue is the gear linkage/shifter is very stiff, particularly in the left/right direction, so the spring loading does centre the stick, it stays put where you move it to.
 
When connecting the shifter cable at the gearbox , one looks like it has some pressure on it bending it down to reach the connection point.  This seems odd but I cant see any other way to route the cables.
   
Any ideas?
 
Cheers
 
EDIT:  The issue was with the bellcrank selector, see below.

And therein lies your problem. Any distortion in the 'flow' of the cable will negate the spring loading due to friction between cable & sheathing. You'll have to find a better path.

Yeah I figured that but I can see another way of routing them, the "kink" appears to be between the body clamp (which is fixed) of the end of the cable gland and gearbox linkage, so no real way to do it different, unless I am missing something obvious.  I will have to compare to another MR2.
 
Cheers

Ok, update.  I disconnected the shifter cables at the gearbox, they run smooth, and manually selecting gears made it clear the issue is with the linkagaes/selector on the gearbox.  I removed the selecting bellcrank (red arrow pointing to it below):
 

 
Once removed the gears could easily be selected on the gearbox and the in out of the selector from the gearbox springs nicely in the 3/4 plane, so the issue is in the selecting bellcrank.
 
The square had some wear so I rotated it 90 degrees.

I took apart the hinge bushings, greased everything up (the hinge was smooth anyway)

 
Anyway, as soon as I bolted the red arrowed bracket to the gearbox the in/out of the selector at the gearbox (or the left/right of the gear stick) stiffened up, so I am thinking the red arrowed bracket is the issue.  Looking at it from the side it's a bit bent, downwards at the free end, so maybe that is causing it to not be aligned correctly and it binds up.  The shift is a huge improvement over before but still does not centre in the 3/4 gear plane.
 
Does anyone have a pic of this selecting bellcrank piece so I can compare?
 
Cheers

Had another play with the bracket and selecting bellcrank.  I ended up putting a washer under the bolt closest to the selector, to effectively lift the end up up a little.  I also reverted back the square to the "worn" orientation, as in the non worn orientation it would bind up when the bracket was tightened.
 
This fixed it and the gears now work a treat!!  I also fitted the Gen3 shifter assembly, the gear change is now fantastic.  The gen 3 shifter compared to the older one has the gear cable pick up 15mm higher from the fulcrum, and is also 10mm shorter overall.  So the movement at the gear knob is significantly reduced.
 
Cheers