1. See what the problem is with the shifting. It could be minor such as a cable or gummed up shifter. It might be wise to keep the gearing (not to mention cheaper) than converting / altering the drive train. That way if you decide you like riding and decide to expand your horizons and ride more or commute, you still have what you need. New less aggressive tires would be a good choice as well.
2. As far as comfort goes, I'd try and do a little research or talk to someone about the "fit" of your bike. The right sized or properly adjusted bike makes a world of difference. Also, you will need some time in the saddle to get reacquainted to it. Try a newer saddle, but saddles are a personal choice. Maybe try a basic WTB or something.
3. Find another bike shop. That will make a great commuter. Tough , rugged and good for any terrain and no suspension. That guy was an ass. I have an old steel Specialized I converted to commuting on and it has proved to be invaluable.
4. Go ride!