I really do not want to get into how to assemble and disassemble apk files here, sorry. There are no secrets in what I do - you could take a look at pretty much everything here:
http://sourceforge.net/p/sonyfmngr/c...AD/tree/prsT1/
This is the script which is executed every time to prepare fully functioning build:
http://sourceforge.net/p/sonyfmngr/c.../build_all.cmd. Note, that odex files are built on the device itself