I thought I would update this thread. About two or three months ago, I started noticing a ton of pods in my system when previously there were none. The amphipods were getting huge and I was even seeing their molts float around the system occasionally. I attribute the initial population increase to an upgrade in lighting that seems to have caused a healthier production of microalgaes. My rockwork was almost sterile looking before. I did also experience a hair algae outbreak (nutrient issue, not lighting) which helped the population to really explode.
Anyway, after noticing the pods were sustained for a little over a month, I decided to try out some more shrimp. I purchased three peppermint shrimp on 8/10. They were all accounted for today and I did find one molt the end of last week. This is the longest I've had shrimp survive in this system. I purchased a cleaner shrimp the end of last week and it seems to be doing well so far. Time will tell if the root of the problem was fixed and I'm not sure I'll ever truly know the cause of my previous problems. I do believe that not having a complete ecosystem and the missing microfauna were at least part of the issue. My tank appears healthier to me (minus the nutrient issue) at least.