Well, this has been quite a wild ride, jumping from one section of RAM to another, following any little byte and being mislead time and again.
First off, the "bad" news. This...
03F315 - C9 44 (Change the 44 to where ever you want the Two-Handed weapons to start)
03F34B - C9 44 (Not sure what it's doing, but it's likely best to change this to whatever value you are changing the above to)
Are actually Left and Right hands. However that 03F315 above is not Two Handed Weapons per se, but is the start of "special" weapons all together. It took me forever in-battle to realize that this was just a starting index, and the first index just happens to be Two-Handed weapons. What does this mean? I'm not entirely sure, to be honest. But if this value is not lower than what you have Bows set to (not sure why you'd ever want that) then you will not be able to equip bows in non-bows/arrows in either hand. So really, it's not a big deal, just don't go too crazy with placements and always keep your indexes aligned, lest any problems appear.
So without further ado, the data!

This one's going to get a little messy (since there's a lot of moving pieces to this one)
in RAM...
- 01BFBD - A2 4D 5F (Index Range of Bows and Arrows, checks this range to see if it is allowed in the recessive hand, use this to add more weapons that can be used in the recessive hand.)
- 01C044 - A2 00 43 (Weapon Must be above this value to be equipped with an Arrow (The game ordinarily uses this value so in theory you could equip Two-Handed weapons with Arrows, if there weren't other checks made to prevent this.
- 01C07A - A2 4D 53 (Index Range of Bows - Unsure, but best to change it to whatever value you have the others 4D53's set to.)
- 01C096 - A2 4D 53 (When changed to a new index, will allow you to equip arrows to selected index Only if the arrows were not equipped in the first place and the other checks had not been modified.)
- 038F27 - C94D (When altered to a new Index, it will add the Attack power of both weapons (Arrow + otherwise) together.)
- 03F315 - C9 44 (Right Hand -(possibly dominant hand) Change the 44 to where ever you want the Special Property weapons to start)
- 03F34B - C9 44 (Left Hand - possibly recessive hand) Change the value to what you have above.)
- 038F27 - C9 4D (When altered to a new Index, it will add the Attack power of both weapons (Arrow + otherwise) together (or divide them depending on which hand it is held) to the left (possibly recessive) hand. Around this are are other various CMP's for Arrows, and Shields)
- 038F41 - C9 4D (As above, except for right (possibly dominant) hand.)
In ROM...
- 0xC1BD - A2 4D 5F (Index Range of Bows and Arrows, checks this range to see if it is allowed in the recessive hand, use this to add more weapons that can be used in the recessive hand.)
- 0xC244 - A2 00 43 (Weapon Must be above this value to be equipped with an Arrow (The game ordinarily uses this value so in theory you could equip Two-Handed weapons with Arrows, if there weren't other checks made to prevent this. Also Special Weapons cannot be equipped with Shields.)
- 0xC27A - A2 4D 53 (Index Range of Bows - Unsure, but best to change it to whatever value you have the others 4D53's set to.)
- 0xC296 - A2 4D 53 (When changed to a new index, will allow you to equip arrows to selected index Only if the arrows were not equipped in the first place and the other checks had not been modified.)
- 0x19127 - C9 4D (When altered to a new Index, it will add the Attack power of both weapons (Arrow + otherwise) together of the right hand.)
- 0x19141 - C9 44 (Right Hand -(possibly dominant hand) Change the 44 to where ever you want the Special Property weapons to start)
- 0x19127 - C9 4D (When altered to a new Index, it will add the Attack power of both weapons (Arrow + otherwise) together (or divide them depending on which hand it is held) to the left (possibly recessive) hand. Around this are are other various CMP's for Arrows, and Shields)
- 0x19141 - C9 4D (As above, except for right (possibly dominant) hand.)
- 0x1F515 - C9 44 (Right Hand -(possibly dominant hand) Change the 44 to where ever you want the Special Property weapons to start)
- 0x1F54B - C9 44 (Left Hand - possibly recessive hand) Change the value to what you have above.)

There's a Lot here, but that's now to be expected with Special Weapons functionality, thank goodness for editors to compound these all into a simple step. Oh yes, I forgot to actually write down the ROM Locations of the Key Items (and Whistle)
0xA597 - C9 1F - Legend Sword (Change to whatever value you'd like.)
0xA59F - C9 EC - All other Key Item Index (Pass and Whistle have two unique entries for some reason.)
0xA524 - C9 ED - Changing this value will change whatever value you set it to, to act like a Chocobo Whistle
And that's that! I may get a post or edit in on arrows tonight (depends how much energy I have left)

Switched my focus. As I had thought, it seemed that the Key Items portion was only half of the puzzle. The rest of it was in very different (and rather obscure) places.

In RAM...
- 01A25C - C9 19 (Legend Sword, Shows up dark "as unsellable" in Shops, change value to desired item.)
-01C2A7 - A2 00 ED (Shows up dark "as unsellable" in Shops, change value to desired items to make them white (Sellable) but don't forget to change the initial index range!)
-01C927 - C9 19 (Prevents you from selling the Legend Sword, change to desired value to prevent selling that item.)
-01C92F - C9 EE (Prevents you from selling any items above this range, can be altered as one wishes.)
In ROM...
-0xA45C - C9 19 (Legend Sword, Shows up dark "as unsellable" in Shops, change value to desired item.)
-0xC4A7- A2 00 ED (Shows up dark "as unsellable" in Shops, change value to desired items to make them white (Sellable) but don't forget to change the initial index range!)
-0xCB27 - C9 19 (Prevents you from selling the Legend Sword, change to desired value to prevent selling that item.)
-0xCB2F - C9 EE (Prevents you from selling any items above this range, can be altered as one wishes.)