I play the PS versons of all suiko games on the console, ntsc us.
This save file has currently around 150hrs in it, the in-game clock flips over after 100 hours.
You are right about the collision with a S1 perfect file, used for an attempt of S2 level building. For the S2 perfect file, I used a subsave of the original, made with lv60 chars at the end.
Actually, I did most of the level-building before the final major battle, so I have five free slots to use. The experience beyond lv 65 is aynwhere the same (10/battle w fortune), so it doesn't matter. And most of the antiques can be farmed out of the gregminster area as well as the majority of rare runes (rage, flowing, cyclone, phero, prosperity, ...) and some final armor (master garb, taikioku wear, gold necklace, star earrings, ...), so this saves a lot of time and serves the purpose for a perfect file with all items/runes effectual. Later, I switched to Gregminster for the rest (crimson capes, power rings, mother earth, thunder, windspun armors, some antiques).
I usually name my castles after final fantasy characters.
The stats of my final party (viktor, flik, rubi, camille, cleo) are boosted with rune pieces and predominantly not the ones you receive by lv 99 alone. Nevertheless, I may post these. I have to look into the file if you like them anyway. And I share your opinion, to refrain from training everyone omnipotent, including magic skills. It removes the individuality from the chars.