You asked for some recommendations? Well, there you are:
The shims for adjusting the end play definitely go behind the drive side bearing race. I have no idea why the service sheet and Haynes manual (I think) say to put them on the timing side also, imho that's nonsense, you've seen the result yourself. If you don't ride it in cold weather, you can shim down to almost zero. I shimmed mine down 0.5 thou. The alloy crankcases will expand much more than the steel crank, so that's absolutely no problem.
2 thou on the timing side bush is fine, like muskrat said. From what you have described (play, noises) I would be surprised if the big ends were okay. Definitely check the journals for wear (measure with micrometer) and regrind if necessary. Very often the cold oil remaining on the bearings disguises the play caused by wear, so it's hard to tell whether they are really worn or not just by rocking the conrods up and down. A play of 2 thou is what you would want here, too.
Probably the timing side crank journal will need to be reground as well. Check this for wear or ovality prior to purchasing a timing side bush.
The bush itself has to be line bored with the crankcase halves assembled with ALL bolts. It's also good to fit the barrels in order to prevent any distortion later on when assembling. The alginment of timing and drive side is very important, so give it to somebody who knows what he's doing.
If the crank is out, you could consider having it nitrogen hardened after grinding. This improves the surface hardness significantly, the EN40B it is made of (learnt that here on the forum
) is very well suited for nitrogen hardening. Also the fatigue and tribological behaviour of the material become better. I had all my cranks, camshafts and followers treated this way, as its not really expensive (3,5 Euros per kg of material here).
Cheers, Markus