I haven't seen this mentioned anywhere, or at least not using a quick Google search, but something about Agent Cooper reminds me of Ronnie Rocket, the titular character in Lynch's un-produced (and brilliant) screenplay.

It's been a long time since I've read it (there are actually two quite different drafts) but in that story Ronnie is an innocent, helpless character, kidnapped by two well meaning but foolish doctors who want to transform him into what they think of as a 'handsome man'.

There's something about Cooper's blank innocence (combined with his physical helplessness) since his return that seems to chime with Ronnie. Add to that the quote from Albert about the 'absurd mystery of the strange forces of existence', which is taken from the title page of the 'Ronnie Rocket' script.

It's such a shame that film never happened but maybe some of the feeling of that story is finding its way into the new Twin Peaks.