Sorry you cant find half your apps. There needs to be a thread on her just to perform FR. You wont be able to find your apps on the market. You will be able to find the first few in the "my downloads" folder, but after 2 or 3 of them, they delete. Did you have astro file manager installed?
Doing a FR is easy, and IMHO, essential to get rid of a lot of problems experienced on the 2.1.
Here are some instructions.
Disclaimer- Everything on the phone WILL GET ERASED...so back up, back up, and back up.
First, if you haven't done so, back up your contacts, pictures, etc. You can use gmail to back up your contacts, and Lookout mobile to back up the rest. You don't have to worry about your SD card because the FR wont affect it.
After everything is backed up and you're SURE of it, either write down you applications, or download app brain in the market. It's just an application to help you remember your apps. If you did have astro file manager, your applications are backed up to the card, and most of them should be there for you to just click on and install.
Now you are ready for the FR. First, shut off your phone. After it is off, hold the vol down button and send key, and then press the power button. You should get a boot menu. Just follow the onscreen instructions and it will guide you through. It's very simple. When it is finished, you will have to reactivate your phone. Everything is easy to follow and will prompt you.
IF .... IF by some reason something goes wrong and you can't activate, DON'T worry. What happened was the lock codes were probably reset to something different during the procedure. Just call #8899 and you'll get technical support and they will fix everything for you. But don't worry, it is a rare occasion.
If FR didn't work for you, chances are you have a faulty device. It seems that FR is solving A LOT, and by A LOT I mean A LOT of problems that people have. Also, its been noticed that if you have a faulty or sketchy device with 1.5, you will with 2.1 and you need a replacement. Verizon is aware of these issues and are very lenient on giving replacement phones.