Changing the boot animation is fine. Trust me all devs expect their ROMs to be modified in one way or another...
You need to use a a root level access file explorer.
Root Explorer is available from the Market for a few bucks.. Nice program and user friendly.
Ghost Commander (I just was informed of this one thanks, Chris41g!) is free from the Market.
You can then navigate to the "system/media/" location and then first rename the existing bootanimation.zip to "bootanimation.bak" so you can restore it if you like at a later date. Then you can copy and paste a new bootanimation.zip into place of the existing. You will have to enable the system to "Read/Write" instead of the default "Read Only" so you can make the changes.
Root Explorer has a button on the top upper right corner I believe to make the change, and Ghost Commander on the very bottom row of buttons scroll to the right until you see "Remount /system". Hit that button to select "RW" mode.
Of course the above is only needed if you can't find a "Flashable" boot animation.
I had incorrectly assumed that the Adao File manager was capable of this. I installed Ghost Commander and was able to replace the animation once I figured out where /sdcard went (it disappeared and I had to use the real directory - /mnt/sdcard).
Thanks for the help (again).
