I have recently been having problems with certain areas in Skyrim respawning enemies even though it has long since been 30 days. I even got a 3 day respawn mod, but still it seems that the respawning link in those areas has broken. Is there a way to mod the game that could force those areas to respawn/reset?

You could try and force them to respawn via the console:

resetinterior <locationid>

Get the locationid of the various interior cells either through the UESP Wiki page for the dungeon you want to reset or by using help in the console. You might also want to play around with the LocationCleared command and see if that helps the cells you're having problems with to respawn.

SetLocationCleared <locationid> 1

Try the Random Encounters mod - it's on the Nexus.