I used Titanium Pro to "freeze" some things plus it's nice cuz it backs up your app's too. Root Explorer is always nice too because you can move things to a new folder if you want, that way you don't have to delete things.
And as far as JT's Rom/Kernel you can get those both, brick free using ROM Manager. Open ROM Manager, hit menu, do Clear Download Cache. Go to Download ROM, select jt1134. Then Super Clean ROM, (it will ask you what other options you want). After that it should start downloading everything you've selected. I'd recommend using wifi if possible it's faster as long as you have your charger near you.
It will ask you if you want to Backup Current ROM and If you want to Clear Data/Cache (I think). If you already did a backup before this you shouldn't have to backup again. But you should clear data/cache, when you reboot after this it will be like your first boot on your phone. You'll have to do the fun setup wizard again, and put all your contacts back in (unless there's an easier way). I had time so i just did it the long way.
That should take care of the Rom, after that whatever kernel you want to use is up to you.