The final problem was trying to get the game working on a real PS2. Creating a DVD DL image for PS2 is different than what one would do for other systems. They essentially consist of 2 seperate ISO file systems, that would be burned onto two seperate discs for a dev system. However, the dual file system creates serious problems for burning an actual dual layer disc. It took a lot of expensive dual layer coasters, but I finally tracked the problem down. When generating the ISOs for a dual layer disc, each layer is set up as a perfectly functional single layer disc. This includes a reserved header at the beginning of each layer. But in a real dual layer disc, there is no reserved header on the second layer. So, to create a properly working dual layer disc for PS2 that can be properly burned, the first 16 sectors (32768 bytes) of the second layer ISO must be completely deleted from the image. Then, you can do a copy /b of the two images to create a single ISO file. Once that's done, you can create an MDS file for the layer break, by taking the final sector number of the first layer and adding one to that (note: layer breaks can only occur on multiples of 16, and so is basically impossible to mess up). Once the properly fixed and combined dual layer image has been completed, it acts just like a real dual layer image, and can be properly dual layer patched.

I hope that explanation makes sense, but here's a step-by step approach.

Step 1: get the 2 ISOs made.
Step 2: load the second ISO in Hex Workshop.
Step 3: Select a block from the beginning that is 32768 dec long.
Step 4: delete the block.
Step 5: save the file (and make some tea while you're waiting).
Step 5: copy /b iso1 + iso2 new-iso.
Step 6: Go to tools>make MDS in IMGburn.
Step 7: Add the new-iso and set the layer break to the last sector number in the iml file + 1 (and set the path scheme to PTP if you really want to).

Enjoy!