Have you used TES4Edit? That is the tool you need to merge the patches onto the originals. The messy thing here is that the UOMPs that are not mergeable are so because they contain new records. The first thing you have to do is find those records and use TES4Edit's copy into as new record option. The rest you can simply drag over and overwrite the originals, by, in the right frame, dragging the changes over on top of the originals. My mind is fuzzy right-now, but I think you can right-click on a group of records in the tree, and use a batch-type command to override the originals with the changes all at once.
Thanks for the quick answer. Funny, the inspiration for this came from your Goole page, ready it all last night. Keep it up, it inspired me to start from scratch (just finished wiping my computer and re-installing Win7 Pro 64-bit. So now I am moving back my mod files and will try using BAIN instead of OBMM. I used BAIN before, only switched to OBMM recently.
So your answer is yes, so now I will read the manual for TES4Edit and see what I can do.