Got my bike in bits since I bought it as a botched but running machine (for 5 years!). When I bought it I drained the g/box oil and a small broken shim washer fell out. I suspect this was the #41 on the secondary shaft from the manual (I use the Evo 2010/11 manual which I have been told is relevant to the 2008 270 motor). I have a couple of questions. I am unsure of the direction of 1st gear on the secondary shaft (see photos - is it 1 or 2). 

Also I have a shim washer #4 on the primary shaft 20mm x 30mm x 0.5mm in the manual but mine measures 1.0mm thick?

 I would assume it would be number one. Did you not take a pic before you took it apart? You should also be able to spin the shafts before you reassemble and see it work.