Trying to fix line-endings with git filter-branch, but having no luck

The easiest way to fix this is to make one commit that fixes all the line endings. Assuming that you don't have any modified files, then you can do this as follows.

# From the root of your repository remove everything from the index
git rm --cached -r .

# Change the autocrlf setting of the repository (you may want 
#  to use true on windows):
git config core.autocrlf input

# Re-add all the deleted files to the index
# (You should get lots of messages like:
#   warning: CRLF will be replaced by LF in <file>.)
git diff --cached --name-only -z | xargs -0 git add

# Commit
git commit -m "Fixed crlf issue"

# If you're doing this on a Unix/Mac OSX clone then optionally remove
# the working tree and re-check everything out with the correct line endings.
git ls-files -z | xargs -0 rm
git checkout .

The git documentation for gitattributes now documents another approach for "fixing" or normalizing all the line endings in your project. Here's the gist of it:

$ echo "* text=auto" >.gitattributes
$ git add --renormalize .
$ git status        # Show files that will be normalized
$ git commit -m "Introduce end-of-line normalization"

If any files that should not be normalized show up in git status, unset their text attribute before running git add -u.

manual.pdf -text

Conversely, text files that git does not detect can have normalization enabled manually.

weirdchars.txt text

This leverages a new --renormalize flag added in git v2.16.0, released Jan 2018. For older versions of git, there are a few more steps:

$ echo "* text=auto" >>.gitattributes
$ rm .git/index     # Remove the index to force git to
$ git reset         # re-scan the working directory
$ git status        # Show files that will be normalized
$ git add -u
$ git add .gitattributes
$ git commit -m "Introduce end-of-line normalization"