I think I was the one that brought up Appbak around here. Appbak let's you dump a text file onto your sdcard of all your current apps. After a full wipe, you can then re-download and install Appbak, then use it to click through and re-download your Apps. Sometimes App restores and data don't play nice with a new ROM. It's rather rare in my experience, but there can be conflicts sometimes. Appbak makes getting your apps re-installed easy, and you have a list to refer to if you think you forgot something.
Besides other benefits, the Pro version of TB allows you to batch restore your Apps. However, you can probably get away with the free version to only restore Apps one at a time that your REALLY want the data for, then use Appbak to re-download and install the rest.
Yes a Nandroid backup is done in CWM, by simply choosing Backup and Restore then Backup. This process stores an image of your system at the time of the backup on your SD card. However, CWM versions 5.0.2.6 and earlier only allow you Nandroid backup to an external SD card. 5.0.2.7 now allows you to also save a backup to your internal SD card. So keep this in mind if you don't have an external SD card installed.
Without messing around with kernel zimages here would be your order of things:
1. Download Calk's Wipeall.zip, ROM and the stock kernel I linked, and move the files over to your phone
2. Do all of the App backups you want to do
3. Boot into CWM
4. Make a Nandroid backup
5. Install the Wipeall.zip
6. Install the ROM
7. Reboot
8. Let everything settle in after booting .. maybe give it 5 minutes
9. Boot back into CWM
10. Wipe Cache and Wipe Dalvik Cache in CWM (may not be necessary but I always do it)
10. Install the stock kernel
11. Reboot
Keep in mind that when caches are wiped, it will take a long time for the first boot, and your phone will sit at the boot animation screen for what seems like too long. Just let it do it's thing, which should take less than a few minutes. If it's taking 5 minutes or more then you may have a problem. Just be patient with it.
Lastly, when installing a new ROM, it's always a good idea to calibrate your battery. I use a free app called Battery Calibration on the market, which is simple and effective. Basically you charge your phone to full, load the app while still on the charger, click the calibrate button, then pull it off the charger. Run the battery all the way down to 1% or even until the phone shuts itself down, then put it back on the charger and charge to full again ... all uninterrupted (no reboots or partial charges) if you can.