The Secret Song is linked to the main albums by the drawing of a chord in a stave in both booklets which is replicated on the disc of The Secret Song. I think that this is probably related to the non-standard tuning used on "several songs" on the albums; I am pretty sure that this refers to the four interludes and maybe more but I haven't looked into that yet.

The Greek words I think relate to four songs on the albums. My guess is Beautiful - They Aren't All Beautiful (I'm ignoring Beauty as this isn't on Bath/LYBM and is only a bonus anyway); Landscape - Geography; Stone - Stones of October's Sobbing; Sleep - Sleep is a Curse.

Also look at the Hebrew lettering in the booklets. Each Interlude has two sets of symbols. One is the name of one of the serphiroth, the "planets" of the tree of life, hence the tree/planets lyric. These correspond to the phoenetic spellings of the same four sephiroth, Binah, Geburah, Hod, Yesod. Each of these planets is also named in English in the lyrics of Birth Pangs of Astral Projection.

"But I know there are mansions out there,
Maybe on Saturn or Mars or Mercury or Luna,
Maybe on Saturn or Mars or Mercury or Luna,
...Maybe this is a clue. "

I have not yet picked through all the of lyrics for other clues.

I don't know exactly what the other Hebrew letters mean in the Interlude artwork but I strongly suspect that they correspond to the paths of the tree of life, each one of which has an associated symbol, number, tarot card etc. I think the numbers are important but I'm not too sure yet. The lyrics of the Secret Song also make mention of using the first words of certain lines. I think the idea is use the Hebrew symbols with the tree of life and produce a set of numbers, then pull a message out of the first lines of the correct songs. It's actually kind of blatant in the applicable lyrics:

"I read into these four songs
The numbers of the lines
In a magical language
And wrote the first words

And this is a great secret "

So still working away! I've tried a little first-wording but only have garbage so far. I haven't looked into the Qliphoth/Tree of Death angle yet. Not sure if that's an angle worth exploring. References to shells, dark aspects, alternative interpretations in the lyrics of the albums would be clues that this is important after all. Note that I haven't googled this or anything, the only clue I had starting off was that the secret song is the key to the puzzle. I only know anything about the Sephiroth because I recently read Promethea...