To be honest, it's a tough call to say for definate what will be right. You'll only know when it "feels" right.
The two shim thicknesses look to be a little out. By that I mean they are usually very close to each other. 1mm is a little too far out.
What you are trying to achieve is to center the crank in the cases, using the shims to firstly take up any manufacturing errors and secondly to preload the bearings slightly.
Your shim calcs are basically saying there is a 1mm machining error or that one of the bearings is out. That's a lot IMO.
Double check everything again, and then once more. Make sure the bearings are seated correctly. Take measurements at 4 or 5 places on the bearings to make sure they are seated flat.
If you are going to reduce the shim thickness, they need to be reduced by equal amounts else you'll move the crank off centre.
If you need any more help, call me on 01623 758877. Unfortunately it's not an easy operation with the bits in your hands, it's even tougher to explain in text. Good old Haynes