assorted questions

Is Silver a dilution?  It actually acts just like agouti in that it restricts black, only more so than agouti.

Yes, Silver is considered a dilution.  It doesn't restrict black it lightens it.  Agouti restricts black to the points.  Silver lightens black wherever it may be it doesn't alter it's location.

Flaxen 'seems' to be a counter to Silver, in that it double restricts color from mane and tail and lightens the body, instead of on black it works on red.

Flaxen doesn't lighten the body only the mane and tail.  It can be present in any color chestnut including liver.  I think you may be thinking of Panagre which does lighten the body and is sometimes present with flaxen (but they are often found separately as well).  

A very dark liver chestnut with flaxen

Is there a theory about what causes different shades? eg light bay, dark bay. llighter/blond chestnut or red chestnut?

In cats these genes are referred to as "Rufus Modifiers" and they are said the control the shade of an animal. The truth is that we don't really know how many genes control shade but it is inheritable at least to some extent.

I know sooty can make a color appear darker but sooty is darker from the top down, (right?) some bays are uniformly light or dark, as are some chestnuts.

Some of horses that were in the past called sooty are now know to be brown. Brown does affect a horse from the top down. True sooty tends to be more evenly dispersed. or affect the lower part of the body more.

Hope that helps some

Sooty Palomino

A very interesting chestnut with flaxen, sooty, and pangare

Another silly question, Do I understand htis correct E means eulamine is present, e means not present so color is red?

E_ would mean eumelanin is being produced and  ee would mean that pheomelanin is being produced. They are completely different proteins with different structures, but yes one is black and one is red.