No problem. I like to flash my way forward with roms whenever possible and then if I want a newer radio or bootloader, I generally flash that in recovery also (if packaged for flash in recovery) or I fastboot flash the img. Anyway, that's just the way I like to roll, not trying to persuade you one way or the other but what I would recommend more strongly is getting away from using any tookits for anything other than maybe the initial rooting procedure or unrooting.
So that said, I would urge you to either download a Jellybean based rom (and it's associated Google Apps (Gapps) package onto your phone directly using a browser, or if you're on limited data, download them to a PC and then transfer them onto the phone's sdcard partition by way of a USB cable. If you download them directly to the phone, you will find them in the location /sdcard/Download. Material goes there by default which is fine because when you flash roms, the files will be accessible at that location. If you decide to use the PC, download the necessary zips to the desktop ideally, then with the phone plugged in, you should notice the phone showing up as a drive (actually a storage device) on your computer...like along with c: d: etc and it'll be labled "galaxy nexus". When you double click on it, you will be seeing the contents of your sdcard in reality because that's the chunk of storage that shows up and you have immediate read/write acess to. So...you can simply drag and drop the rom zip and the Gapps zip onto the card. Once fully transferred, you can exit out of that window and unplug the phone from the pc.
Now onto the rom flashing portion. Being your first time flashing, you will have to power off the phone, then press and hold both volume buttons along with the power button to enter the bootloader. Once there, use volume up toggle your way to recovery and then the power button to enter recovery. If you are flashing a brand new rom, perform these steps in the clockwork menu:
1.) Wipe data (factory reset)
2.) Wipe cache partition
3.) Advanced menu > Wipe Dalvik Cache
then...
4.) Install zip from sdcard
5.) Choose zip from sdcard
6.) You can now navigate/locate your new rom and any gapps package
7.) Flash the rom first. When it's done, immediately flash the gapps package.
8.) When all of that is done, choose the reboot system option and the phone will restart with the new rom installed. Be aware that the first bootup can take a long time (up to 5-10 minutes but generally less) so don't interupt it if you're at the "Google lock screen" for a good amount of time.
So now you'll be setting up the phone again like it's new...i.e. entering your Google credentials, choosing various phone settings like ringtone, wallpaper, notifcation, etc etc. Also the only apps that will be there are the system apps along with any other apps that the rom developer baked into the rom by default. Because of this, many of us purchase Titanium Backup from the market which allows us to backup all our apps and their associated data. Then when we flash a new rom, we go straight to the market, download Titanium again, and it will recognize our phone by a special file it drops into the sdcard. We then have the option to restore all apps and their data. Now, in Jellybean (and maybe ICS also I can't remember), there is also a built in option on the phone to backup settings to Google servers. You can also get your apps back that way along with perhaps a few other phone settings but personally, I've found that to be slightly hit and miss so I still use Titanium and I skip the onbaord backup option. Up to you.
So in a nutshell review...get the rom and gapps you need onto the sdcard one way or another, then boot into recovery to wipe and then flash.
Couple parting caveats:
Once you are on a given rom, if the developer releases a small update, sometimes they will recommend a "dirty flash". In that event, you can just wipe cache and dalvik cache and avoid the data wipe. Then you won't have to worry about setting everyting up again. Apps will still be there, settings in tact, etc. Rule of thumb is to listen to the developer's advice on which route to go with. This won't be the case for your initial install as you will be effectively moving from ICS to Jellybean with your rom flash so a full wipe is absolutely required. Moreso just mentioned that for future reference.
Also, once you're on a custom rom, there are most generally extended reboot options that inculde the ability to go straight to the bootloader or recovery. So the powering off, pressing volume buttons + power thing will no longer be necessary.
Any other questions just ask, we are here to help.
