I replaced the apk with one from Jellyshot (4.2.2 gapps and 4.2.1 gapps) and still had the problemFor the message "system process not responding", it is caused by gapps (googlebackuptransport.apk more exactly). We will update them for next release. If you need a workaround, try to change googlebackuptransport.apk in /system/app/ from another recent gapps . Anyway, that message doesn't affect anything in daily use.
For OTA app, update notifications can be effectively disabled (except at boot) in next release
Can you upload the googlebackuptransport.apk from your ROM please?
Thanks