From what I've gathered, it's looking more and more like a staging
recontact issue related to first stage engine shutdown behavior,
possibly exacerbated by the near vacuum of the staging environment.

The only other possibility would be complete staging failure related to
the upper stage engine nozzle change out, but that seems unlikely.

I hate staging : http://webpages.charter.net/tsiolkovsky/

I don't hate much, but I hate staging.