I stopped trying to learn Japanese a long time ago, but in terms of transcription, this is (fairly) simple stuff. Mostly kana, with only a few kanji. Most of the key contextual information appears to be in the text though, not the pictures. I consulted the text for help with some of these transcriptions, either by searching it to see if they were also in the text, or running it through Google Translate for context. Still, I'm bad at reading handwritten Japanese, which lacks the absolute distinction between characters that typewritten fonts have, so there may be errors in the parts I wasn't able to get a dictionary definition for.
So the first linked page is apparently about imagining what happens after beating Lavos at the Ocean Palace.
Text near Magus: ピキッ
Magus thought bubble: あっ (Ah!, Oh!, or hey!)
Text near Lucca and Marle: ひょいっ
Text near Magus: ひゅ
Magus thought bubble: 兄上 (big brother)
Text by Schala: もじもじ (bashful sound)
Marle: ん (Huh?)
ベロロ~ン (slurp)
ケロケロ (ribbit)
Those mini-Lavoses are called "Petit" (プチ). Viewing the story on the second linked page via Google Translate, it looks like it's an AU where Petit crashes down in Guardia shortly before the Millenial fair and is adopted by Crono. Another page about Petit (not part of the fanfic) says that Lavos died in space, leaving Petit to crash down alone.
Text by Petits: チャチャチャ: cha- cha
Crono: プチュ
Petit: プチッ
Petit: プチ… (petit...)
Petit: プチー (petit)
Petit: プチー (petit)
Text by Crono: ドナドナドナド~ナ~ (Dona, Dona)
Petit: プチ (petit)
Continuing on, the destinations of the Zealians, except Janus/Magus, are mixed up. Belthasar is in the present day, and taught Lucca. (He also appears to be responsible for the temporal scattering disaster.) Together, they build the Epoch, using Dreamstone that Petit literally shat out. Crono still gets framed. After escaping, they join Belthasar and Lucca and go on a time journey. Schala is the first queen of Guardia, Melchior is a weaponsmith in prehistory, Queen Zeal took over 1999 A.D. and lives on into 2300 A.D., and Gaspar is in 2300 A.D.
Interesting stuff I suppose, but we haven't had the resources to get all the official material translated, much less random fanfics.