Merge OTA update with Stock ROM

[bver]

I'm coming from WM and new to Android/Linux, so I apologize for the noob question, but are there any resources or tutorials explaining how to merge an OTA update with a stock ROM. I've extracted the stock ROM using dsixda’s kitchen, but I can't figure out how to combine (or add) the OTA updates to the stock ROM. Esentially, I'm trying to build a custom ROM, based on the stock, but including the recent OTA update. I've searched everywhere, but no luck. Any help or direction is greatly appreciated.

Calkulin seems to have done what I'm asking here: http://forum.ppcgeeks.com/showthread.php?t=126944