My difficulty with referring to Manning now as female is that most of the actions which I care about were from when it was PFC Bradley Manning. It's like anyone who changes name partway through a major news story. Chelsea Manning is in prison now, but saying "As an intelligence analysis, Chelsea Manning had access to classified files and got into disputes with her chain of command over both work-product issues and personal conduct." seems incorrect.

If this had been known before the news story, no problem at all. It's just hard to use "Chelsea Manning" or even "Private Manning" to refer to actions undertaken far prior to this.

Ironically I think this was one of the things bradass87 brought up in chats with Adrian.

PFC vs. Private is just as complex. I think there's a military way to deal with that (because ranks usually do increase); e.g. in some contexts is it "Captain (now Major) Snuffy..."