There are always some variables... if you have a vigorous boil, or a dry kitchen, you might have boiled off more water than the instructions assume. For extract, usually you top up afterwards to your target volume. So you could have added a little water to get to that gallon mark.
As for your siphon, contact Northern Brewer. Their customer service is top notch, and I'd be surprised if they didn't offer to replace it or otherwise fix the problem.
The bubbles? You're good. Usually, you add yeast, maybe a day or so later start seeing bubbles, then the bubbles finish up after anywhere from 4 days to 2 weeks. It's yeast, it can't tell time... it just does its thing. The time thing is less dependent on volume than it is on yeast health, beer strength, and how much yeast you've added. Be sure, though, that the yeast is still doing important things, even if you don't see bubbling. It's metabolizing compounds that lead to off flavors, settling out and clearing the beer. Ideally, you would check with a hydrometer to make sure you're done, but my usual advice is to wait three weeks, then bottle, if you're not sure. Adding time doesn't hurt, but bottling too early can be risky.
Look into temperature control- I have a feeling your closet may have been a bit warmer than we usually try to brew at. Warmer=quicker fermentation, too...
Welcome to the hobby, and ask as many questions as you need.