I sent a similar private message .... here is a post that I hope some of you will find useful.
I successfully applied the OTA from 4.4.2-->4.4.3 on my N10.
My setup
- Nexus 10 (running rooted kitkat, 4.4.2)
- clockwork mod restore rom
- SuperSU (the paid version)
- BusyBox free by StericDroid
Initial OTA failed because of an incorrect MD5 in build.prop. I did not make many changes, but it is nice of google to tell you why you are failing OTA so you can address it.
My Path in Summary (details follow)
1) Restore my build.prop file to factory stock (NOT THE WHOLE IMAGE, just the file)
2) Apply OTA
3) Reboot from CW restoring root
4) Reinstall BusyBox
I'll expand this a bit since I had a couple of stupid problems like the OTA no longer tried on to download and I did not keep a copy of my original build.prop file around.
0) in SuperSU select Settings|Survival Mode (paid version)
1) Restoring build.prop (if you have your original use it -- I did not have it)
-) on my linux box: download the factory stock 4.4.2 for Nexus 10
-) tar -zxvf <file_downloaded>
-) cd to created dir, then unzip the zip file (creates system.img, ...)
-) linux: install some tools: sudo apt-get install android-tools-fsutils
-) process system.img: simg2img system.img system-out.img
-) mkdir ./mnt; mount -o loop system-out.img ./mnt
-) grab ./mnt/build.prop and put it on my Nexus in the /system dir
2) Apply OTA
-) I downloaded to my Nexus 10:
-) ttp://android.clients.google.com/packages/ota/google_mantaray/f9195e9c509dbbaa734df03138b11b7f66a7f09d.signed-mantaray-KOT49H-from-KOT49E.f9195e9c.zip
-) I rebooted my Nexus into the recovery rom
-) I'm using ClockWork Recovery ... Select "Install zip | from file ..." follow your nose to select the downloaded OTA from where you saved it (in my case /sdcard/Download/<that_long_zip_file_name_above).
-) I backed out and rebooted from within recovery mode. CW will ask you if you want to keep root -- I very surprisingly said "Yes"
3) Final steps
-) rerun "BusyBox" Select "Install"
I was done. Root intact. settings intact (except for build.prop), all data intact, just an upgrade.
I did not disucss how to copy over build.prop, but I'm assuming that if you have a rooted nexus you can do it. A refresher -- /system is a read only file system, so from a shell I did the following:
-) su -
-) mount -o remount,rw /system
-) use cp to copy build.prop to the /system dir (back up your custom one

.
As I said before I hope others find this useful.
Enjoy.