Lymes is a common one people have used the Beck Protocol for and with good success. The others I don't have reports on. However it is important to understand the various theories of how electricity in the body works and how various diseases work in order to come to a conclusion whether this would be of potential benefit.
I urge you to read "Healing is Voltage" by Jerry Tennant. It is the most current and plausible theory of how and why it works.
Aside from that, I recall a bench study from India several years ago. I am unable to find the information again unfortunately. In their experiments they showed that gram negative bacteria responded to electricity much better than gram positive. It so happens that gram negative bacteria is the very bacteria that modern medicine seems to have a problem with. Bartonella for example, is a gram negative bacteria. I think the protocol may very well have a good impact on Bartonella. When it comes to SIBO or cystitis, those are more deeply internal conditions that I believe the protocol will help, but I think more would be needed.
Bottom line is that the Beck Protocol seems to have an effect on pathogens of all types and when these are addressed, it frees up the immune system to eliminate what it needs to eliminate.
In regard to doing Hydrogen peroxide therapy at the same time, I hesitate on this one because of what hydrogen peroxide is, I do not believe I would combine these therapies myself or advise anyone else to do so.