My apologies for coming late to this thread -- and late to the world of Alfa Romeos! My experience has been 23 years of service to another European marque's transmissions. My thoughts, please take with as many grains of salt as you wish.
Unfortunately the method of bluing will not give you meaningful results. The problem is that taking a pattern as you've done does not simulate how things will actually load up and center under engine load: with the engine pushing one way, the road forces and drive train friction pushing the other. These forces moves the contact center on the pinion and ring gear teeth. When properly measured by the factory (well, the ones I am familiar with) to minimize mechanical noise, the pinion depth is done in a rig that creates load.
Normally my experience has been that, barring particular circumstances, you do not need to measure and adjust pinion depth. The particular circumstances that would make it desirable to measure depth include changing the ring-and-pinion set, machining to the case, or of course some previous service that made a mistake in shimming (and that happens...).
Kudos to you for measuring with a CMM! I hope this is helpful and good luck with the project. It seems (from my brief acquaintance) that getting quiet running of Alfa pinions is a persistent problem.
You're not late, you are perfectly on time, many thanks for your reply.
In the particular case of this box, I don't know how it was done at the factory, but I do know that the pinion does come marked with a number (in cents of mm) which can be used to reset the depth to the correct factory value.
However I don't have the tools which would allow me to do this.
Failing that I can only try to reassemble it back to what it was before, a state at I know wasn't producing any noises or anything out of the ordinary.
I did take care to measure it in the most accurate way I could access, thanks to a friendly colleague at work who helped me out.
I was very surprised to see the depth change so much, I have no explanation for that. I did notice the shim was quite heavily marked, it had these deep grooves (I could feel them with my nail) which only went away after I took about 0.03 to 0.04 on each side of the shim. You can still see a trace of it in this photo:
This was a little surprising because the shim sits between the two flat surfaces of the 4th gear inner race and main bearing race as seen here:
I know someone had opened this box before so who knows...
Either way, regardless, the depth is now set to what it was before (within tolerance), the pattern looks okay-ish so I think this will be it untill the car goes back on the road...