I have a GEN 2 MR2 turbo, It came with a non-lsd E153.
 
I brought a GEN3 E153 LSD and it came with the passenger / left side cv shaft, 
 
I did research before I brought the box and I thought only the passenger side shaft was different, and the drivers side / right side cv shafts were the same for lsd and non-lsd.
 
I have the box installed and the passenger side shaft in but the drivers side shaft does not go in all the way, I didn't want to force it as the drivers side shaft doesn't have and circlip on the end, usually they just slide in, I have worked on many E153's but not a GEN 3 one, is it possible they run a different shaft??

I have a set of both gen2 and gen3 shafts sitting in the shed and I'm possitive one side is the exact same. I just cant remember off my head which one. I'll check tomorrow when I go out.

Its the right side shaft thats different.  It wont fit.  I think the left side shaft may be slightly different but still fits. You'll need the part of the axle that has the intermediate bearing on it from LSD car.

I thought it was the other way around James? When I installed an LSD E153 in my gen2 I needed to buy a new passenger side axle stub (short one) and re-used the long one with the bearing on it.
 
 

My gearbox came with the short / passenger shaft, 
 
After doing some research it appears the GEN3 LSD uses a different shaft, so now I need to find one.

both sides are different. if you want it to work and last like it should, fit the proper axles

Have a look at the Monkey Wrench website