We have a repository that was exported from subversion into git. This repository is used by Mac, Linux, and PC users. Needless to say the line endings are a mess. Some files end
This related SO question will be of interest to you:
Trying to fix line-endings with git filter-branch, but having no luck
And here is a link to similar advice from Github.
Also, as mentioned in Greg Hewgill's post it is wise to verify that future committers use an editor which handles the new line-ending policy correctly.
When you say "Adding autocrlf = true seems to fix things slightly." I assume this was done in using .gitattributes.
I would try, as much as possible, to standardise on a common line ending to be used throughout all source files in your project. A good one to choose might be LF only, however I would check that the editor(s) used by developers handle your chosen common line ending sanely and correctly. (In this case, sanely means not changing every line in the file just because the user changed one line.)
You may need to do a big cleanup job and have one big commit that changes all the file line endings to your chosen standard ending. This will be awkward but probably not as awkward as maintaining a variety of different line endings.