After some discussion and testing came to the conclusion that there is indeed a problem with the endgame phase as you end up with no way to get more weapons and a likely huge army of enemies lined up. The folowing is a simple solution.
Instead of placing enemies drawn in the Find phase to the bottom of the deck. You start a separate pile with them. When you deplete the deck shuffle the used item and enemy cards from battles and start drawing from that for the Find phase and draw from the enemy stack for the Flip phase. You will continue to get gear and this makes the whole thing play out faster too.
This method may make things a little too easy so you might want to play that Bosses do not suffer damage reduction when attacking.