Ok - I've been modifying, remodifying, reorganizing, and testing
pretty much my whole solution and I think I've identified more
closely the issue.

I thought the issue  before was with content  Types, but the problem  is
being caused by the ContentTypeBindings of my Site Feature. I'm
trying to bind several custom content types  to the Pages library
(which is instantiated somewhere in the Publishing features, I
haven't been able to track it down yet).

It looks like the error  I'm getting ("File not found") is because it
can't find the Pages library path I'm giving it in the ListUrl
property of the binding. Not sure how to fix  the problem, but I think
I found  out why from MSDN:

"Content type  binding enables you to provision a content type on a
list defined in the onet.xml schema."
(msdn.microsoft.com/en-us/library/aa543598.aspx)

In my onet.xml schema, the Pages library/list isn't defined because
it's added by one of the Publishing Features. Does anyone have an
idea on how to fix this? I've tried adding a <List> item in onet.xml
to instantiate a Pages library (at worst thinking it would give me
some form of "already exists" error), but did nothing.

Well I've gotten around this issue  and thought I'd post my results.
The ContentTypeBindings to the Pages library was causing the issues  I
had. I believe this is because the Pages library is created  at the
Web Scope, and Content Type Bindings are set at the Site Scope. Well,
even though MSDN does not list ContentTypeBindings as being at the
Web Scope, they do work there - and that's how I got around this
issue, by moving the CTB's to a Web scoped feature.

(Elements by scope  - http://msdn.microsoft.com/en-
us/library/ms454835.aspx)