> 1. I got a vertical line where I asked for a decrescendo.

That happens when the horizontal space for the (de)crescendo is
too short, especially if it begins or ends with a dynamic indication
which shortens the hairpin. The minimum length should be larger than
zero and if necessary, the overall spacing should be increased to
give room for a readable symbol. You could experiment with setting
the paper variable crescendo_shorten to something less than the 
default 4.0 * \interline;

> 4. Lyrics and \fermata collide. I know that the TODO has lyrics and scripts
> colliding; I'm just including it here because it's really an issue for me
> with fermata. Other scripts aren't a problem for me, but sometimes I need
> fermata on both sides of the staff (when sop and alto hold different notes,
> for example). In fact it's not just scripts and lyrics: In a choirstaff,
> scripts above the bass clef collide with scripts below the treble clef.

A workaround until this is automated is to set the maxVerticalAlign 
property, the problem is that you'll get the extra distance on all
lines, not just where you have the collision.

> 7. When it's a tight fit to get all the notes in the first line, the first
> note collides with the time signature. Is this the same as one of the
> spacing bugs mentioned in the TODO?

You could change this in the space-alist defined in lily.scm.
I sent a patch to Han-Wen with some changes to the spacing 
parameters and he included all of them except the one that
solves your problem in 1.1.57. My suggestion is to also 
make the following change:
@@ -106,7 +106,7 @@
    (("Time_signature" "Span_bar") . (minimum_space 2.0))
    (("Key_item"  "Span_bar") . (minimum_space 2.5))
    (("Staff_bar" "Time_signature") . (minimum_space 2.0))
-   (("Time_signature" "begin-of-note") . (extra_space 1.0))    ; Huh? see twinkle.ly
+   (("Time_signature" "begin-of-note") . (extra_space 2.5))    ; Huh? see twinkle.ly

   /Mats

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