I am in the same boat. I am doing it becuase I like to learn and have never tried anything like this before, basically my goal right now is to build just one application (Phone Alarm is what I chose) into a rom so I can say I know how to so it from almost scratch, then I may think about doing something more in depth.
Here is what I have figured out and can share, please I am a noob, so anyone feel free to correct me or point out an easier way, I am not giving complete instructions there are instructions on how to use the tools in the threads that supply them.
I first downloaded the updated rom from my carrier (TELUS), then I opened the file in winrar to extract the RUU_signed.nbh file, then I used nbhextract on the RUU_signed.nbh to seperate that into the a bunch of .nb files. I am only interested in the OS.nb and I used ImgFS Tools Version 2 convert that to a bin and to create the dump(basically seems like a listing of all the files, folders etc... in the rom. Then I used bepe's package tools which seems to put it all into OEM and SYS folders. That is basically as far as I have completed. From my understanding the next steps seem better documented IMO but also seem to be the most complex and time consuming (took me 3 noob man hours of reading and fiddling just to get phonealarm ready put in) and I haven't completed the rest of the steps but they are listed in the wiki
http://wiki.ppcgeeks.com/index.php?title=Kitchen under the heading Creating an OEM Package.
Like I said I am a noob, but I think I'm on the right track. I wouldn't have even answered this for fear of giving wrong info but I have had a lot of difficulty getting help myself trying to tackle the bare bones of this is definately not cake and after going through the work of getting phonealarm cooked in....I'm not sure if I will continue to try and make my own roms or not.