[mdeal]

I did just this back in December. To remove the rod from the flapper I took a punch and knocked it back through the box/flapper door. This was easier said than done. It also mushroomed the tip of the rod. I just took the rod to a bench grinder and smoothed it back out for re-installation. If I remember correct, mine was rusted pretty bad in there and it was a bear to get out. When you re-install it there is a flat side on the rod to help position it back in the correct location.
Patience. You'll get it.