The materials you obtain during the Dana (past) parts are automatically transfered back to Adol's inventory in the present once you finish her parts. Those materials aren't even of any use to Dana since she cannot use or trade them anywhere. The only inventory items worth editing in Dana's inventory (save 001) are the stat boosters (Power, Defense and Life Elixer), the item that increases your lvl by 1 (Tempest Elixer) and Essence Fragments (the currency in Dana's part). Those don't carry over and are hard to get in Dana's timeline. Save 002 has Adol's inventory with more than 0 of all the materials and medicine and such.
Edit: I've found the location of the important items in Dana's inventory:
The 01 is for Tempest Elixers
The 00 05, 00 04 and 00 05 for Power, Defense and Life Elixers (respectively)
The 00 35 for Essence Fragments
Give me a minute and I can most likely get you Adol's inventory too.
Edit2: This is Adol's inventory of save 001 (including the 6 Thick Hides)
https://imgur.com/a/XCdPMC1
Adventuring Gear is probably too risky to edit, since they're key items.
@Slade.AU
A lot of these games are using pointers (there's base address and anywhere from one to dozens of additional offset addresses that "point" to the memory location that stores the value). These can change each time you enter / leave a room, every few minutes, or not at all in the same game session. It depends on the game / developer / engine the game is running on. The next time I look at the game, it's going to have different memory locations for the same values. I guess the only way to find out is to use a hell of a lot of the items and see if they drop from 999 to 0 really quickly ! I used a couple of items and they all went down by 1 per use, so I think everything worked out fine! I also played ahead a little bit to see if anything crashes but everything seems to be in order. Thank you very much for this, now I can finally finish the game without having to grind for ages. 
I didn't know there was a big difference. I thought the only difference was that with RAM editing you didn't have to dump and inject saves all the time but instead you could just edit stuff while playing. I didn't think that addresses would be different.
All that empty space is probably items Dana isn't supposed to be able to get. The game swaps between Adol's time (present) and Dana's time (past) and they each have their own inventory. Adol's inventory can obtain every item and material, but Dana can only get about half of them (she doesn't need all those things). Dana's inventory is automatically transfered to Adol when you go back to Adol's time.
I was able to inject the file without any issue, and you left Dana right next to a crystal that lets her teleport to the room she was in before.
I've attached a program to fix it and the source for the program.
At around 0xC0B4, the location of where the game stores if you found/bought an item is located. This is important if you want to add items yourself. From what I can tell, the game uses 6 out of 8 bits per byte. An example to add: thin, thick, beast, and ancient hide.
The save attached gives you all items and some debug items as well.
@
Xdqwerty:
