I wouldn't worry much about the low reading. Since this is a tried and true recipe, if you followed the instructions then the gravity should be close to what it says.
It's easy to get incorrect readings if the extract is not mixed in enough. A few other reasons. Don't use the plastic tube the hydrometer came in. Get a hydrometer flask. They are cheap enough and the hydrometer won't stick to the side. Spin it around in the flask to get all the air bubbles out. Try to take the reading with the wort at 60°. The hydrometer should have come with a conversion chart for different temps though.
Good work checking the hydrometer with tap water. The exact test is distilled water at 60° but your tap water is close enough.
Keep the red cap on the bubbler, it does let the CO2 escape. I fill mine with cheap vodka even though it isn't really necessary. Most of my little red caps seemed to have disappeared so I just use a piece of aluminum foil.
EDIT: One more thing. The yeast will find the sugar on the bottom but there is no reason you couldn't have swirled the fermenter around slowly to mix it up and the yeast is probably bottom fermenting anyway.