You can have some caffeine but they recommend you keep it limited. Drinking 6 cups of coffee a day would probably be a bad idea! But the 2 you had were just fine. As far as chocolate, that is a dumb one as far as I'm concerned. There's not enough caffeine in it to do any harm unless you are eating like 10 bars a day. The biggest issue with caffeine is actually that it is a diuretic, meaning it makes you have to pee a lot. Pregnant women already have enough of that problem! Which is why I steared clear of caffeine during pregnancy. Anyway, as with most things in life, moderation is the key.
Interestingly, with sushi, my doctor explained that the problem with it is more related to parasites. If you pick one up, it won't hurt the baby but they can't treat it because the medication for it would hurt the baby. So you pretty much have to live with it until after you delivery. GROSS! I am an avid sushi eater but the risk just didn't seem worth it to me. Even though the chances of picking up a parasite is pretty low, it would just be my luck that it'd happen to me while I was pregnant!
Anyhow, at the end of the day, my doctor always reminded me that there are women living in 3rd world countries who are delivering their babies in rice fields who do just fine. We have access to the best medical care in the world and our doctors know the most so they give us their best recommendations for a healthy pregnancy. But just keep in mind that there are babies in the NICU right now being weaned from crack. So when you put it in that perspective, that babies can survive being born addicted to crack, I don't think a couple of cups of coffee is much to worry about.