aquaarche,
The heterotrophic bacteria we use is a product called Stress Zyme by API. I don't know how they grow it. It does a great job in our system.
My experience with bio-filters is limited to pH neutral expanded clay (Hydroton). I really shouldn't be giving advice on bio-filters that are designed using other materials. I can only tell you what I have read in articles and posts on forums such as this one. Using gravel works well for many. Others have had problems with pH due to the high alkaline content of the stones found in the gravel. It may be that this is what you have experienced with your system. This was one of the reasons we chose Hydroton.
I can understand that many just don't have the budget allocated to their Aquaponics system to purchase some of the rather expensive items that would insure a greater probability of success, or the products are not locally available. We have chosen to build a system that would avoid most of these problems by attempting to design it based on the many years of experience of others. We had no idea what we were getting ourselves into financially, but once involved we decided to reallocate precious funds to assure success. What we have learned is classic; that is to say, if we had to do it all over again we would do it somewhat differently.
It has been an expensive lesson, and in a sense, we are starting over again by building a grow house while still maintaining a rather cost intensive greenhouse year round. This addition is setting us back financially even more but we hope that it will yield enough positive results to have made the investment worth it. Our goal is to be able to learn how to grow fish and food in a sustainable way with the least amount of operating cost. It has become clear that there is an economy of scale, for there is a minimum size of system that can grow sustainably. It also requires a minimum number of people to operate it. That size is much larger and uses growing techniques that are somewhat different from your typical backyard system. Also, the initial investment is quite high. We will eventually be investigating some of these techniques in our grow house.
I see that you have other posts on this forum and that is where you should be looking for answers to your questions. I am sure there are others here who have had similar experiences to yours and hopefully have figured out the cause and solutions that may help you with your system.
Oliver