Wil, you're right, "specification reform" is a nightmare, and I think you've described a very confusing situation pretty darn well.
One point is worth noting/clarifying.
Re:
"AIA absorbed Fasteners [Bolts, Nuts, washers, pins, etc] using NASMxxxxx P/Ns that closely paralleled the original P/Ns... but still retained the "old" ANxxxx/MSxxxxx/MIL-x-yyyyy/etc P/Ns in order to minimize transition confusion [IE: AN3--AN20 are now specified as NASM3--NASM20]."
The AIA (NASC Committee) has gone to great lengths to carry the identical part numbers forward to "new", replacement "NASM" Standards/Drawings. In general, only the prefix on the Specification/Drawing itself has changed (i.e. The "MS1234" Drawing/Standard "transitioned" to "NASM1234"

. However this was/is not, in general, carried through to the hardware part numbers on that standard -- which remain exactly the same. (That is, even though the standard/drawing changed from “MS1234” to “NASM1234”, the part number remains exactly the same: “MS1234-1”; not “NASM1234-1”).
I get calls from people thinking that the "NASM" Standard/Drawing prefix automatically applies to the part numbers, and they need to revise hardware part number callouts to reflect this. It is hard for some people to accept that the part number format on the drawing does not necessarily have to reflect the format, or prefix, found on the drawing/standard controlling that part. We're very used to seeing it that way.
However,
In the vast majority of cases (perhaps all) for AIA “NASM” Standards, the actual part number (hardware) callouts on the "replacement" drawing are unchanged from what they were on the "original" “MS” drawing. Check the drawing and any associated cancellation/supercession notice.
This is obviously not the case where a government part was “replaced/superceded” by an existing “industry” standard part. These parts, however, will not generally be found on “NASM” prefixed standards. Once again,
check the drawing and any associated cancellation/supercession notice.