The solution was so simple!  The bootstrap.php file in each of my module root
directories started with a lowercase "b" instead of "B". 
Zend_Application_Resource_Modules is hardcoded to look for
/modulepath/Bootstrap.php.  Now my modules are loading perfectly.  It took
so long to figure out because I was setting the bootstrap filename for the
default module specifically with a lower case "b" in the config ini.

The other thing I fixed was moving the main bootstrap from being directly
under my application directory into the root of my default module.  I
removed the extra autoload function from my Module_Bootstrap since I was
getting duplicate autoloader instances for my module.  The default module
still needed to by autoloaded even though it was under the module directory.

I hope this helps others to avoid lost days and lost hair.

Shaun
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