Hey, I'm actually an indie dev and your description reminds me of a project a colleague of mine made way back. It was called 'Lair of the Wyrm', sort of a tribute to the old pixel classics. I think only a few hundred people played it since it was made …
Man, I feel ya. Debugging can make you wanna smash your keyboard. What engine you using? If it's Unity, they got the Profiler tool that's super handy. It shows you where the bottlenecks are. Otherwise, break down your update methods and see if you've got code that can be moved …