[krisfris]

You're right that the voiced and unvoiced pair ð and θ probably belong together, as is the case with other voiced and unvoiced pairs. This would also significantly reduce the disambiguities that need to be manually resolved in Step 3. I chose to put θ into category 8 though because intuitively it sounds more like f than t to me, possibly because I'm not a native speaker. I might change my mind about it if it turns out to be more practical to have them both in category 1.

I like your idea of using the major system as a form of steganography. It would require a deterministic encoding algorithm though. I might explore this idea in another post in the future.

[cjhveal]

I think these are cases where it's going to depend on what is most natural for each individual, especially when used for mnemonic purposes. Whether the acoustic or articulatory similarities feel more salient is going to depend entirely on your own mental model of the language. It's common to see the unvoiced dental fricative realized as /f/, even in native english dialects, so if that is more natural for you to remember, there's value in that.