Geranium kisser (Geranium meaning soft and stimulating, so a soft kisser)
Skin like silk and face like glass (Their skin is soft and they have a very clear face (since glass is clear).
Don't confront me with my failures (?)
Kiss me with your mouth open (Talking about how they kiss)
For your love, better than wine (Saying how his love is better than wine)
For your cologne is really fragrant (His scent really arouses her)
Call on me, call on me, call on me (?)

I have a feeling that this song is about the relationship of a couple who on the outside, look pretty good, but on the inside, have many problems dealing with their lives (But our bed is like a failure.)

beautiful, beautiful song

My thoughts; a couple who looks good externally, while intimacy is a big problem and causes issues in their relationship.
I agree with organic joes.

thought it was "all day up in the valley" not 'family'
not positive though, i guess.

"For your cologne is sweetly fragrant" is the line. This song is beautiful, by the way. Dave's guitar line is deceivingly simple until he adds in the tuplet clusterfuck to end the line.

The 'don't confront me with my failures' line is from 'These Days' by Nico/Jackson Browne; the guitar part of this track sounds similar to the Browne song, so I would guess it's an intentional reference.

This seems pertinent:
http://www.songmeanings.net/songs/view/122805/

This is Angel, right? Or am I mistaken and this is Amber?

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Seems like the lyrics are a collage of all their influences.
"Geranium kisser / Skin like silk and face like glass" is definitely a reference to Bob Dylan's 'Sad Eyed Lady of the Lowlands' ("...And your flesh like silk, and your face like glass..." / "...are waiting in line for their geranium kiss..." )

"Don't confront me with my failures" is from Nico's 'These Days'

"Kiss me with your mouth open / For your love, better than wine" is most definitely a reference to Stephen Duffy's 'Kiss Me (With Your Mouth)' ("Kiss me with your mouth. / Your love is better than wine.)

And 'Call on me' could be a reference to Stevie Winwood's 'Valerie'.

There's probably more, but I have a headache from listening to Stephen Duffy and I'm going to sleep.

It may seem like a dubious explanation, but if you listen hard, you can hear a bit of all these
songs on the record. Bob and Nico's folk guitar, Nico's violins, Duffy and Winwood's beats and synths. And this wouldn't be Dave Longstreth's first musical referencing (Rise Above, anyone?)
He is not one to adumbrate his influences.

Oh and "To the chamber that conceived me" could be from Solomon 3:4,
"It was but a little that I passed from them, but I found him whom my soul loveth: I held him, and would not let him go, until I had brought him into my mother's house, and into the chamber of her that conceived me."

...I've noticed several of those references, but I don't think the song is only a pile of favorite lines with no story, there's definitely a story involved. And the sound is beautiful, overwhelmingly reminiscent of Nico's style.

The narrator's 'failure' makes me think of her inability to bear a child. The obvious sensual texture of the lyrics feels like her trying to persuade her lover that they can have sex for the sake of passion, and not think of the 'bed' only as her failure. Then the final stanza seeps into far more rooted concepts. 'Geranium killer' is a soft twist of mood, intentionally to show her discontempt(?) as though she blames him. 'Throat of soil and mind like stone,' he can plant seeds (lies) in his mouth without thinking. 'Please don't defend a silver lining/around the halo of what is already shining,' asking him to not see their (her) failure, but rather the love, the passion they have. Then the planets align for just one afternoon that never ends. (Does he kill her for her failure?)

Definitely one of the most intricate, and gorgeous songs of their catalogue to date.