A couple more recommendations...
I would definitely look for a hotel/motel on the Red Line. It will make getting around a lot easier.
Check out the Plough and Stars in Cambridge. They've recently gone a little more upscale, but they are a great irish bar with amazing food. It's one of the best kept secrets in Cambridge. If you're into beer, it has some of the best Guinness around. They're halfway between Harvard and Central Squares on Mass Ave. It's about a ten minute walk from either the Harvard or Central T Stop.
Toscanini's ice cream in Central Square is some of the best ice cream around. They usually have about 20 flavors at a time, but they have hundreds in their repertoire. I used to work there, and I never got sick of eating the ice cream. Even the vanilla is excellent, but they have some crazy flavors like earl grey and nocciola.
If you want to hear live music, go to Toad in Porter Square (on the Cambridge/Somerville line). It's right across the street from the T. They have live music every night and there is never a cover charge. The restaurant next door (Christophers) is pretty good.
Personally, I think that Fire and Ice is both overpriced and expensive. If you do go, watch out for the drinks... the prices are STEEP. It's where they make most of their money.
The duck tours are pricey, but they are a great way to see the city.
If you like chocolate, go to Burdick's in Harvard Square. They're on Brattle St. The hot chocolate is really, really rich but it's also delicious. I would stick to a small. It's very filling.
It's really cold here right now, so bring a hat, gloves, scarf, warm coat, etc. If you're from Florida and not used to the cold, it can be a bit daunting. My sister moved to CA a few years ago and now, whenever she comes home, she spends the whole time shivering.
If you want to get out of the city, try the commuter rails. Make sure to print out the schedule, though, because the trains don't run regularly.
If you like vietnamese food, try Le's Vietnamese restaurant. They used to be called Pho Pasteur (which is what most of us locals still call them). They have restaurants in China Town, Allston and Harvard Square. Reasonably priced and quite tasty. They're known for their pho (soup), but pretty much everything there is good. Try the fresh summer rolls (the steamed ones) and their limeade.
If you like funky/vintage clothes, check out the Garment District near Kendall Sq. in Cambridge. That place is huuuuge and they have some amazing stuff. It's worth checking out all on its own. The first floor is called Dollar a Pound and you pay for what you buy by weight.
That's all I can think of right now. Have fun!