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All the spacers are labeled and no I haven't seen them wear to the extent that you're describing however I have come across spacers that have obviously been shaved to bring their end float within spec rather than replace it with the proper 'letter'. Also I agree with Dale to an extent, if its a rebuild (which it seems like it is) from an unknown builder then I'd go ahead and replace the torrington bearings but to be honest for engines I've built or those that are a known quantity I rarely, if ever, do this.
I'm pretty confident this is an original engine, it had 3 pc apex seals. I couldn't find any evidence of anyone having been into this engine, then again I don't have the trained eyes like an experienced builder.
I am going to go ahead and order new needle bearings, it can't hurt.
I thought it was odd that it measured so far out of spec.
Make sure the needle bearings aren't pinched. When installed correctly the spacer should be level with the needle bearing. It is very easy for it to catch the side of the needle bearing and not sit down all the way. Try it again. If the end play is still too tight try a d or e spacer. You ideally want the end play at least at .004.