So are you running Skyraider or just trying to get a custom boot animation to replace the stock 2.2 one? Anyway, my memory is fading on stock (if that's even the case here) but go to:
/system/customize/resource and look for VZW_bootanimation.zip
Once you get the new animation, rename it to VZW_bootanimation.zip and change it out with the one that's currently in that file location using Root Explorer while in read/write (R/W) mode. Reboot and the new animation should be there without the need for any wiping.
If you're actually running Skyraider and wanting a different boot animation for it, make a nand backup first, then apply the new animation without a wipe. If any problems, revert via nandroid.