I do not have experience with the red tail shark, but from what I understand they are relatively aggressive, but mainly with their own kind. Guppies might be pushing it. Dwarf gouramis can probably handle themselves.
Your good bacteria are present in numbers based on the amount of ammonia (food for them) that is present. When you removed the fish, the bacterial colonies decreased due to the reduced ammonia in the tank. I think this die-off takes a couple of days, but I am sure you are "cycled" for the red tail only by now, and you will need to add more fish gradually, or get Bio-Spira and add them all at once. It is good that you thought of this, because I don't think a lot of people would have thought about it at all.