You should really notice a slight drag of the rear brakes with the lever pulled just one click, but 2 to 3 isn't bad. After you've changed pads, you need to pump the pedal several times (w/ engine running) to get the pressure back up, b/c the pistons haven't come back out yet. Just giving one firm press isn't the way to do it, although it may get the job done, best to give several moderate pressure (and distance) pushes on the pedal until it firms up close to before the change.
Some service manuals don't mention this, not sure if all Hondas are supposed to have this done or not, but on some cars you're supposed to loosen the e-brake cable before you pump the brakes up, following pad change, and then tighten up the cable again and check that it's working correctly. However, I think skipping this step (assuming e-brake is properly set to begin with) will just prolong the time before it adjusts and works perfectly, after it's driven a little.