When going to a custom rom you need to doa full data wipe unless you plan on starting over and doing a full data wipe.
Phone needs to be factory clean when going custom otherwise problems are not only expected but guaranteed.
Everything from language errors to market not working or even anything google not working, random reboots and crashes, its a really bad idea to not do a full wipe.
I fail to see how this has anything to do with Back-up and restore of APK's?
When you root (Before the wipe) you can back up system APK's(/system/app/*) with titanium and that includes OEM/SP installed apps. Once this is backed up you can copy it onto the SD card or PC. That is how I kept the Route66 that came with my DHD or even the Games that was preloaded on my Xperia Play.
After the flash you simply enable side loading and install the backed up APK file.
Granted that the app dont work on all ROMs and you need to dig deeper when developers used the android.os.Build.MODEL or such API but there are workarounds.