After looking at Bosola's great notes and some trial and error, I've replicated the patch for other PSX versions (I wanted to patch the Japanese versions, I only patched the kernel myself, but don't see why it wouldn't work for scene.bin as well) I wrote this quite quickly but should be a good guideline..
1. Open Bosola's US patched ISO in CDprog and check the movie dir's LBA and size for KERNEL.BIN and SCENE.BIN (this saves some work doing it yourself)
2. Note that null1min.dat has been deleted in the US Patched ISO (this file is for making the game run on really old PlayStations).
3. Open Japanese ISO (or another version, I'll just call it the JP ISO from now on) and delete null1min.dat from the movie directory with CDProg. Using CDProg again create new file called KERNEL.BIN in the movie directory with the same LBA and size values as the US patch's KERNEL.BIN in the movie dir (if your also applying SCENE.BIN, do the same for that file).
4. Extract yamada.bin from US patched ISO and open in hex editor (you will want to check the values).
5. Extract yamada.bin from JP ISO and copy down the values for the KERNEL.BIN and SCENE.BIN according to the directions in this thread (you will be copying them from the values of the US's yamada.bin - don't copy all of them, obviously - just the scene.bin and/or Kernel.bin): http://forums.qhimm.com/index.php?topic=9737.0
6. Using CDMage import your modified yamada.bin into JP ISO, followed by your OWN (or JP original) kernel.bin into the new kernel space on your movie directory (if its smaller than 64kb, it will just be padded and still work).
7. And your done.. at least for disc 1.
8. For discs 2 and 3, you will probably want to check the values from the US patched versions 2 and 3 (those versions may even have two NULL files, see if they are deleted in US patch, I haven't checked it myself).
For testing I used modified kernel.bin to see if it was successful (battle message), but if you don't have one - just opening your equip menu and getting into a few battles should be enough to test it. If CDmage says you can't import over the kernel.bin in the movie dir you have done something wrong and need to start again. If the game doesn't boot but works absolutely fine via save states you've also done something wrong but getting close
One thing I'm not sure about is my original KERNEL.BIN still exists in the Init directory. Whether you delete that or not is up to you I think, I don't think it can harm anything?
Have you added much data to your KERNEL Bosola, how does it hold up?
I took a look at applying the magic defense bug also, but seems a lot a more work with armor pointers and stuff..