Follow these steps:
1) Search > Find In Files...
a) Search for: (the identifier name of the function that caused the problem when you did references)
b) Look in: <Workspace>
c) File types: All Files (*)
d) Match case: checked
e) Match whole word: checked
f) Match color: unchecked
g) Click on "Find"
2) Navigate through the search results and hit Ctrl+Dot to try to do a push-tag. Basically alternate between Find-Next (Ctrl+g) and Push-tag (Ctrl+.) until you hit a case that seems really slow. (keyboard shortcuts may vary based on your emulation, you can figure these out).
3) When you find a case that is really slow (note that it might not actually be a reference to the original function, it might be some other function with the same name in another class). Then put the cursor on back on that symbol, click the mouse in the message bar to reveal the SlickEdit Command line, then type the command "codehelp-trace-push-tag" and hit enter.
4) The trace will go to the SlickEdit debug window which should show up. Click on that window and then hit Ctrl+X to cut it's contents to the clipboard. Then paste that to a plain text file and post it here.
The location of the slow push-tag might help you narrow down where things are going wrong in order to trim things down to just a few files.