The Stinger and Type-Y139

They aren't the same. That file is worded extremely bad, and there is no other source that mentions "Type-Y139" as the model number for the Stinger.

Prior to launch, the Project Umbrella staff had a rather lengthy discussion on this topic.  Here is the July 16th Passenger's Diary excerpt from Resident Evil Zero which NewsBot just mentioned:

This paragraph just doesn't make any sense. If anything, it's incredibly redundant.  Here is a translation of the Japanese version provided to us by WΣlsh:

This doesn't really help matters.  The Archives glossary, however, states that the Type-Y139 B.O.W. was "made from shelled creatures that are never seen in the game but are written about in the file Passenger's Diary.  Going on the weak points outlined in this file, it is thought that they were the basis for the B.O.W. Stingers."

Given that the Archives book, despite its numerous flaws, has proven to be much more reliable than any of us once thought, I think that pretty much settles it.  The only question that remains is just what the hell was the Type-Y139?  Personally, I believe that this might be it:

(Note: You can find this image at http://www.survivhor.com/RE1/BETA01/PERSOS/19/index.html)

It looks like a mutated Blue Crab to me, and you can see why the creature's head carapace might have been a liability.  Something else to consider is the U(Ultimate)-8 from Resident Evil 5.  That hideous thing looked like some sort of bizarre arachnid/crustacean hybrid.  Could it have been the culmination of Umbrella's earlier experiments with the Stinger and Type-Y139 B.O.W.s, along with Tricell's plagas?   Just a thought...   

(http://projectumbrella.net/articles/U-8)

(Thanks to http://www.residentevilcenter.net for the U-8 scan!)

That's an old translation. First, there is no crustacean T-virus, just T-virus. The second line reads, "Type-Y139 is no different [from t-virus influence on the other crustaceans]".

In other words, Type-Y139 is the creature described in the experiment. The scorpion on the train is simply an infected crustacean and the file hints at its evolution.

Also,  the investigation team goes to the training facility to see what's left of the "abandoned speciemens", not experiment.

A scorpion however is an arachnid not a crustacean.

This is a weird area as well, I mean one assumes that they are supposed to be the same and to an extent perhaps the developers ultimately intended this to be the case, but they simply did not do enough research.

I've always been of the opinion that Chimera's theory is the most solid. Unless the translations say otherwise I think they are different BOWs. Remember it's not the first time a BOW is talked about in files and never mentioned. The MA 120 Hunter from the RE2 Ex files being a prime example.

The website claims there are top-secret B.O.W. given no dev code. Perhaps the scorpion is one of them.

Could be the case, but I'd think a scorpion creature would be fairly low on the secrecy ladder, given the existence of Tyrants (which all had dev codes and were known about however), Nemesis, Ivan, T-A.L.O.S. and the likes. It could be Capcom hand-waving it, but canonically that's just make Umbrella a very schizophrenic company.

Is this image just fan-made, or does it have significance ?

I've been reading the PU translation of the Passengers Diary, and there are that many parallels between the research observations made by this file's author and the anatomy & weakness of the Scorpion B.O.W for me to be more comfortable with the theory that would make the image above correct; the crustacean reference is not so inconsistent with the similar physical anatomy of a scorpions hardened outer body.

It's fan-made.

The point of the file was just to mention that crustaceans have overall a common response to the t-Virus. Type-Y139 isn't anything in particular, it's a random code for a random crustacean they likely didn't even decide on what species it was. Could've been a lobster for all we know, we'll never find out so trying to guess at what it could be is pointless.

The "Report on B.O.W." file also mirrors the other file's point about crustaceans, only that was with an incomplete t-Virus and was meant to show that no amount of dilly-dallying improvement upon Progenitor would make it possible for crustaceans to become viable weapons.