One thing you really need to think about is visibility. Drivers are not used to seeing bikes around in the winter, especially at 3am. I know you say that you have lights, but I'd really make sure that those provide visibility. You might even use one of those reflective vests, especially if there was snow on the ground. I commend you for doing this at 3am. That takes grit.

As far as clothing goes, there are a lot of great resources out there that you can find with google. Layering and head/neck warmth are key. Keep your head warm, even if it takes two hats or a hat and a balaclava, scarf, whatever you have. Use wool or polarfleece - no cotton.

I use a pretty simple waterproof polyester/nylon outer and then varying layers of polar fleece underneath. For hand warmth I do basically the same thing using mitten shells with gauntlets designed to have a liner on the inside. Then I just use cheap liners or another pair of mittens. It usually doesn't get cold enough for me to have to wear another layer over my jeans, but when it does I just have a pair of nylon zip rain/wind pants that I bought at EMS. If you start to sweat then just shed a layer.

Bringing your bike indoors may prevent your chain from freezing while it's parked, but it won't keep your derailleur from freezing in cold/wet weather, especially on a 28 mile commute. Hopefully it's pretty flat and you can live with one gear. I'm going to convert my snow bike to a single speed this fall for that reason.

Then there's the maintenance issue. Snow, ice, and whatever they put on the road is murder on your parts. I have to do a lot more maintenance in the winter than during the warmer seasons. I've also found that an oil based lube is better than the other ones like teflon lubes. That's just my perception - I'm not a great mechanic or anything.

Other than that, just keep at it. That first cold day in the Fall don't skip the commute. Cooler Fall weather will slowly get you used to the cold so that it's not such a shock. If you stop commuting for a day, it's easy to stop for two days. If you stop for two days, it's easy to stop a week. If you stop a week, well, you can see where I'm going here. Just keep at it, learn what works for you, and good luck!

ps - I've never encountered problems with glasses fogging. It's pretty dry here in Colorado though. You can buy anti-fog rags or droplets traditionally used in ski or swimming goggles.