The lack of characters/foreground folder is totally normal. CLANNAD Side Stories doesn't use any character sprites, it only uses backgrounds and CGs. If you check the game on VNDB you'll see that it has the "No Character Sprites" tag. Side Stories was originally a light novel, so it seems they just colorized the illustrations from that novel and combined them with reused CLANNAD backgrounds and audio from the existing Drama-CD adaptation to make a quick VN adaptation without having to create new assets.
Those script errors are extremely weird. I've searched through the scripts and no "trypoint001" command is used at any point. However, the third line of the third episode's script (SEEN0003.scr) is "label entrypoint001", which just a bog-standard label command. So I guess VNDS is somehow skipping over the first eight characters of that line?
No "his" command is used either, but the third line of the menu script (main.scr) is "text
@this product is a work of fiction. There is no relation between real people, groups, places, incidents or occupations.", which is just a normal text command, so I guess in that case it somehow skipped over the first seven characters and interpreted the "his" as the command.
Have you tried deleting the cache folder? It's possible that recreating the ZIP caused the cache to become outdated. If VNDS fails to detect this (which can sometimes happen), it won't rebuild the cache and will carry on using the outdated cache, which usually causes things to break very badly. If that doesn't fix it, can you send me your script folder? Maybe something got corrupted somehow.