I know with no recovery yet and no backup of my phones original set up I went ahead and changed my boot animation using rom tool box pro with no problem. I then went ahead and changed the font on my phone and it works too. Next tried to change the boot logo but couldn't.
Other then that I am not screwing around any more with it until I get a backup now.
I wouldnt mess w. boot logo at all, but as far as bootanimation, you dont need to use an app at all, its safer this way...use a file manager like Root Explorer.(mount system as r/w)...go to /system/media -> make a copy of bootanimation.zip, paste it to your sd card and rename bootanimationold.zip -> Now you can replace that zip w/ a custom one, but they need to be specified as far as resolution/FPS 480x800, and i believe 30 fps should run fine on our nice GPU.
make sure your custom one is named exactly bootanimation.zip
As far as the audio....in the past its always been /system/media/ui/bootsound.mp3 BUT on our phone, i dont see that file, I do see /system/sounds/power , poweron , poweroff (sounds like the stock bootsound) Therefore leads me to believe for now we can do the same as above and put custom bootsounds there but name them EXACTLY as stock ones were. Beware , since we dont have CWM and cant just flash a .zip, be careful doing it manually.
EDIT: Since you say that it changed fine, via that app....check the paths i listed for the sound files, and see if they are the sounds that you hear/installed as a bootanimation so then we would know 100%, i havent changed a sound yet ill test it tonight.
heres a link to one i like

android vs apple
https://dl.dropbox.com/u/65761686/bootanimation_landscape_480_800.zip
remember to rename it.