How do I restore my iPad apps?

[GAMEROFDEATH]

Ok, so I bought a new iPad 2 and was happy with it until the microphone stopped working. I brought it to the Apple store and got a new refurbished one for free. Yay, right? Not so much. The day before, I had updated my old iPad to 4.3.3 after being on 4.3.1. So it apparently backed it up in the progress. Then, when I tried to bring over all my apps and everything to the new iPad, it only synced the music, photos, mail, contacts, calenders, videos, WiFi, FaceTime, YouTube and Safari. The apps are nowhere to be found. While searching the internet for help, I noticed that no one had my problem. However, they did the exact same thing as I did except for one little detail: after updating, they performed another backup. So here's my question: to restore my iPad apps, should I have done a second backup before and now I'm pretty much screwed unless I download them from the app store one by one, or should I update the current iPad (4.3.1) to the latest version, then restore from backup and maybe my problem will be miraculously solved?