The cycle is Ammonia, Nitrite, Nitrate. You will always have it as decaying food and critter waste will produce the ammonia but your biological filtration should run the conversion quickly enough that there is no build-up of either ammonia or nitrites in the water (therefore undetectable). Water changes (be sure to stir up your bottom substrate and give your rocks a blowing off with a turkey baster) are the only nitrate removal in your current system. I think I mentioned that shrimp are especially good at creating ammonia

. Since you are seeing nitrites, your original cycle and the biological filtration that was created was likely weakened when you removed the LR without time for more bacterial build up with the increased bioload. This will be a little tricky to control for awhile and adding back LR that is fully cycled will help since you need to build up more bacteria but keep the water as nitrite free as you can (which will slow down the new cycle but keep the animals healthier).