The new inventory menu of Project Zelda Engine already has all those things Skylink offers. And has more slots than Skylink!:
To note that the only difference between Project Zelda Engine and Skylink is that in Project Zelda, all the swords are gathered to just only 1 slot (new/upgraded Swords will replace the older swords, etc), which in my opinion is better, as this offers the player/game developer the flexibility to create as many swords as he likes to do, without worrying if there will be enough slots for extra swords. And from what I see, in Skylink you can have only up to 3 swords, 3 shields, etc, while in Project Zelda there are 5 or more swords, without any limits at all.
About the transformation masks: Is easy to create them in Project Zelda. Just all what you have to do is to create them yourself as I am not planning to add them in the game myself, as many people may find the masks unsuitable/unfittable in their games. But as you see, there is enough space in Project Zelda Engine to have up to 8 Masks (If you assign them to the Quest Status Screen) or 4 masks (if you assign them to Inventory Screen, or 12 masks if you use both screens. So anyways, the options and the free space in Project Zelda Engine is limitless and allows you to make it fit in your needs
The Project Zelda Engine has by far much more space for your needs. As you see, it has all the 21 (!) songs in the Quest Status Screen, while in Skylink (no offense, just a friendly comparison) I notice only 12 Song slots. I am just telling you that the Project Zelda is trying to have almost all the "necessary" items while giving some space for your own items as well.
Anyways, if you want to change the new Inventory / Quest Status layout of Project Zelda Engine, it is easy - just edit it with Photoshop or another painting program, and make the necessary edits to the Inventory's script which is not hard to understand. :-)
See how many upgrades there are in total for: Sword + Shield + Flippers + Gauntlets + Tunics. They shouldn't fit all in a OOT-style Equipment Screen, they are too many. Should they?
Also look carefully the medallions, there are more Medallions found in Project Zelda Engine's Quest Status. More specifically, 2 more than in OOT. Those 2 Medallions represent the 2 missing elements from Ocarina of Time, which are Earth Medallion from Earth Temple and Wind Medallion from Wind Temple. Those 2 temples are located somewhere in OOT's Hyrule, however are unaccessible in OOT, but are accessible in Legend of Zelda: Wind Waker, which is the sequel to OOT (200 years after)