Oh, geez. Been a while since I had a doujin that really left me confused like this, but I'll do the best I can to clear it up.

The exact identity of Futo and Tojiko is a common source of speculation of course, and this particular doujin seems to go with the idea that Futo is actually Mononobe no Moriya (rather than Moriya's sister Futohime, who I suppose either didn't exist or was the same person or something). This page makes a joke about doing the same sort of scenario with the Soga, making Tojiko into Soga no Umako, who Futohime was actually married to. At least that's the only way I can make sense of this, and still leaves some gaps. I think the last doujin I saw by this artist was similarly confusing, so I guess that's just par for the course.

Basically, the point is that Mononobe no Moriya secretly became a shikaisen with Prince Shoutoku, while the vengeful spirit that Prince Shoutoku sealed was actually the collective grudge of the Mononobe clan and not Moriya himself.

As for the strange writing on pages 6 and 40, it's actually the same bit of text, except in the former it's written in the Woshite syllabary, a most likely made-up ancient writing system (Jindai moji). Seems to be a quote from "Futomani", one of the main Woshite texts (heh... Futo). In the latter it's written in modern hiragana, symbolizing the switch from "old" to "new history". The actual meaning is still incomprehensible though, or at least I can't make any sense out of it. Wonder if that explains the spell I couldn't translate too.

Translating doujins I don't fully understand myself always leaves me vaguely uncomfortable, but oh well. At least the gist of it comes across even without getting all this meta stuff.