For mistix and anyone else interested in fixing bugs:
I got the two bugged quests working by changing the script named 移動用画面 in the script editor. Looking at the script you should see a block of text like this:
MOVE_LIST[0] = [["首都パルティナ",190,0,0],[2,25,42,8]]
MOVE_LIST[1] = [["パルティナ山道",191,191,192],[12,89,38,8]]
MOVE_LIST[2] = [["千年樹の森",181,181,182],[25,20,68,8]]
MOVE_LIST[3] = [["銀髑髏団のアジト",187,187,0],[11,10,39,8]]
MOVE_LIST[4] = [["ザガン渓谷",210,210,211],[26,8,58,8]]
MOVE_LIST[5] = [["山賊のアジト",69,69,0],[7,48,32,6]]
MOVE_LIST[6] = [["害獣の洞窟",201,0,0],[39,19,39,8]]
I've placed a portion of the first line in bold to point out where the switches that control map access are. As I understand it, the first switch makes an area visible, the second makes it accessible, and the third deletes it from the list. Having a 0 in the access field seems to mean a map is always accessible so long as it's visible, and a 0 in the deletion field means it's never deleted.
This text block is after my changes, which allowed me to complete the two broken side quests without serious problems. Previously the broken quests had different switches listed for the first and second fields, I just changed the second to match the first.
While this fix is very simple, I don't plan to distribute it myself because a) I'm not sure how I could do so except by redistributing the entire game, which seems pointless because b) these quests are totally unrelated to game progression. You are really not missing much by having them broken. Neither of them has any h content and both consist of a single small map with a couple of enemy encounters and brief dialogue. If you are stuck in the game after sneaking into the castle, keep traveling back and forth between the starting village and the castle village. After 5 times the plot progresses. Other people in the thread are reporting successfully completing the game. These bugs are dumb but not game breaking.
So there you have it? If there's an overwhelming outcry to make these boring optional quests playable I'll figure out a way to distribute a fix, but no one is really missing out on much.