Since you are seeing life growing on your rock you should be doing just fine. The ammonia spike comes from dead things decaying and, as Shipposhack noted, your rock likely has experienced its major die off before entering your tank. With the visible life, it means you have a healthy bacteria start (without it you have dead rock and not enough die off to cycle). Do not, however, assume you have a fully cycled tank. This assumption causes the infamous "new tank syndrome" where beginning aquarists over stock an immature tank, causing more waste than the bacteria can handle and killing off almost everything in a short time. The pepperming shrimp won't produce much waste, dead or alive even in a very small tank (unlike a dead, meater shrimp). It will, however, help control any aptasia the rock may have.
Unfortunately, we don't have hobbiest test for what should be there, only minimal test for what should not. It occurs to me that it would be a good graduate studies experiment to come up with a simple method of determine a way to test bio-load handling - might even be profitable, depending on what could be marketed.