Now, when galaxy initializes, it isn't looking in the right location for eggs (or they aren't placed in the right spot on my system). I was able to manually install several of the eggs and the galaxy startup would move to the next egg until here.

Some eggs are out of date, attempting to fetch...
Warning: MarkupSafe (a dependent egg of WebHelpers) cannot be fetched
Traceback (most recent call last):
  File "./scripts/fetch_eggs.py", line 37, in <module>
    c.resolve() # Only fetch eggs required by the config
  File "/Users/galaxy/galaxy-old3/lib/galaxy/eggs/__init__.py", line 345, in resolve
    egg.resolve()
  File "/Users/galaxy/galaxy-old3/lib/galaxy/eggs/__init__.py", line 195, in resolve
    return self.version_conflict( e.args[0], e.args[1] )
  File "/Users/galaxy/galaxy-old3/lib/galaxy/eggs/__init__.py", line 226, in version_conflict
    r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch )
  File "build/bdist.macosx-10.9-x86_64/egg/pkg_resources.py", line 588, in resolve
    The `plugin_env` should be an ``Environment`` instance that contains
pkg_resources.DistributionNotFound: numpy==1.6.0
Fetch failed.