BH2 Theming / Deodexing ?

Where to start.
History...
This is for the Galaxy ROM R11 by BH_MAN on the BH2.

Ok I pulled /system/framework/ and ran

Code (Text):

1. java -jar baksmali.jar -xo (.odex file)_out/ (odex file)

for all .odex files in this folder. then ran

Code (Text):

1. java -Xmx512M smali.jar (.odex file)_out -o classes.dex

then dropped the output classes.dex to its respective jar file via ARK. needless to say when I pushed the new deodexed files over to the phone it didn't work. I'm trying, more or less to get a deodexed services.jar functioning. any ideas? or could someone point me to BootClassPath file so I could check out the dependancies of the of the framework files.
BH_MAN said this happens because baksmali/smali breaks the framework.jar /.dex can anybody help with this?