Is is possible to change / modify the custom ROM you're about to install on your rooted Galaxy S2 (9100)?

Usually, I would install [CyanogenMod 10 Nightly build][1]. Then, I'd install [GAPPS (google apps)][2]. Lastly, I'd restart and it would work.
 
Now, what I want to do is to replace a default CM (CyanogenMod) apps (SMS, Contact manager/Call manager) with those included in [JB 4.1.2 (leaked version)][3].

Is there any way to achieve it?

Thanks in advance for any info and suggestions.

  [1]: http://download.cyanogenmod.org/?type=nightly&device=i9100
  [2]: http://wiki.cyanogenmod.org/wiki/Latest_Version#Google_Apps
  [3]: http://galaxys2root.com/galaxy-s2-roms/leaked-official-android-4-1-2-rom-with-root-for-galaxy-s2-gt-i9100/