I used to do this and use categories, don't like pages upon pages of apps. Haven't had much time lately to redo it all. I basically used all the knowledge gained from thos forum to ssh and swap stuff out. Don't forget to back up files or you'll hate yourself.
winterboard still crashes occasionally even with the mobilesubstrate changes. on my personal iphones i change everything, sliders, bars, icons, any theme type changes manually, no resources usage that way. i save all my changes, duplicate the folders off phone, then if i have to restore i can just dump them back in.
I had mine done manually before winterboard was ready for 3.0. It takes a lot of time, but Poseidon79 is right, you can change just about everything except the wallpaper background, it will stay black.
Basically you have to replace each Icon.png that resides in each prgram folder. Example: /applications/AppStore/Icon.png
You would replace that Icon.png with your custom icon, using the same name. Then for lockscreen, strings and other stuff, you need to replace those also (/System/Library/CoreServices/Springboard.app)
It's a lot of trouble for what I think is not necessary. Winterboard has been stable for me and I have not seen any performance issues.
yeah, i did it yesterday manually, i averaged around 40-45 megs free, and i did a complete restore last night, set up as new phone, and and using winterboard today and i am averaging about 5 megs less. not not that big a deal i guess.....