Well, I'm kind of confirming your list as I'm going through the game right now and so far you're missing a Mythril Shard on a chest in the Cliff of Deep Jungle.
Btw, what do you mean by, for example "chest at the Clock Tower available at 9:00"? Does the hour change in the Neverland Clock Tower? I've never returned to the place since I only did speed runs until now.
Sorry I haven't checked this thread in a while, but here is a guide about the clock tower doors
GameFAQs: Kingdom Hearts (PS2) Clock Tower FAQ by YSF but you only really need to know this:
What is the mystery behind the Clock Tower? Well, you can obtain 12 good
items from here- some are valuable like Megalixir, AP Up, Power Up and
Defense Up.
After sealing the keyhole, return back to the clock tower. You might sometimes
notice a small white light shining above a door on either one side of the
tower. Fly to that door to obtain an item. Every game hour after that, another
light will appear above another door.
To summary it, only 12 doors out of the so many doors contain an item inside
it. The opening of the door is indicated by the white colour light. When and
which door have lights appearing above it, depends on the time displayed
on the clock and the game hour. Enter the main menu to check your gaming time
to keep track of the time elapsed.
For example, if the game hour is 25:00, then the clock will point to 1:00 and
the 1:00 door will open. To convert the time on game hour to the time on the
clock, simply substract either 12 hrs or 24hrs. It's the same LOGIC as
converting the 24 hour clock from the game hour to the 12 hour time for the
clock. See below for some examples.
Game Hour Clock Hour Conclusion
--------- ---------- ----------
A door will only open when the clock time is ?:00 where ? is between 1 to 12.
There is no way you can make the time on the clock to go faster than the game clock. That means it is impossible to get all the 12 items at one go.
To obtain all the items, you need to visit the clock tower at least 12 times. To complete this quest, you need more than 12 hours of time.
24:00 = 12:00
24:30 = 12:30
25:00 = 1:00
26:45 = 2:45
30:15 = 06:15
(You can not do this after that certain point in the game at which the Phantom appears at the clock tower. you must defeat it to continue opening the doors.)
Edit: I found another error. The second Jungle Slide Course gives an AP UP instead of an Orichalcum. Also you get the Dark Matter from completing the third Jungle Slide Course, the last two courses give a Defence UP and a Power UP.
And another one: You get an Orichalcum by beating the Pegasus Cup alone instead of the Hercules Cup.
Yeah I found that those where incorrect as well, I'll fix it up my original post.
I think they where the original games' item locations.