"why did you recommend just checking just plugs 5 and 1?"
LOL. Do the cheap and easy ones first. The Cylinder 5 misfire could be due to problems in Cylinder 5 or 1 (as the engine uses a wastefire system, i.e., 5 and 1 fires at the same time.). If that does not solve the problem you may check the rest of the cylinders too.
"For a side question, can misfire codes be stored in the computer without activating the CEL?"
Most probably not. But sometimes, if it is intermittent (or pending), it might not light up (yet).
