There are many other strange and terrifying things in this layer of storm and sky. 

He flies around for a while longer. When he returns to the primary entrance, it's in the form of a celestial lantern (O-233) with at-will teleportation across unlimited distance. 

The doorway is sealed shut.

Yep. Demon-spider time. He crawls across the planes and arrives in a room of facility sixteen that isn't sealed against teleportation.

Everything is as he left it.

He walks over to the laboratory for form testing. The walls of that room are made of magically hardened stone plus an additional metal layer. If one of these forms is innately destructive, it shouldn't harm the rest of the facility.

Most of the forms are weird and horrifying but don't have any particularly powerful or novel abilities. 

Within a few minutes he gets around to testing the humanoid entity from the screaming sky.

The humanoid entity from the screaming sky is a construct. Its outer shell is formed from a strange ceramic material which surrounds a mass of magically animated non-biological muscle. It's impossibly durable and invulnerable to all attacks except for pure blunt force. Thrice per day, it can increase its strength to an incredible level for a few seconds, exceeding even that of a titan.

Once per year, it can alter reality as though it had cast a wish spell.

What the fuck. Why is the solution to the Great Work a random mindless bipedal construct. How does that make any sense.

He needs to test this—perhaps the construct has the ability to trick anyone who assumes its form into thinking it can alter reality in such a manner. He runs over to a storage room containing, among other things, nonmagical jewelry.

This storage room hasn't been opened in a long time. It's dark and dusty.

He turns on the lights with a mental command and starts rifling through the drawers for a spare ring.

There's a few rings around. They're fashioned form a variety of materials; gold, silver, iron, et cetera.

He grabs the silver ring. It's not magical.

He draws on the well of impossible power within this form. How would the ring like to be a ring of major spell storing?

The silver ring suddenly has a strong evocation aura.

His mistake was clearly expecting the world to make sense at all. He forgot that it doesn't. Sure. Why wouldn't it work like this. The Great Work is finished and he doesn't know how to feel about it. He's not even sure what the next construct number to assign is. Constructs are rare enough that the facilities have only encountered a few dozen ever.

Can he alter reality some more?

Once per year. He will have to wait.

If he shapeshifts into a celestial lantern and then back into the impossible construct—

Once per year. The magic isn't recharged by becoming something else.

He figured as much, which is why he made a ring of major spell storing. He can put shapechange into the ring and have someone else turn into the construct and alter reality to create a scroll with more wishes. Those wishes won't have unlimited experience to spend, because there's a limit to how much magic any single item can have, but they can conjure simulacra who can then shapechange with the ring and alter reality. He could scale that forever, if he wanted to.

Technically this is not a full solution to the free experience accumulation problem because it can't give experience to a creature directly but who cares. The ability to conjure arbitrary magic items basically sidesteps the entire reason behind wanting to grant experience in the first place.

He has decided that he wants to feel very excited about this development! He will need to pull someone trustworthy out of the memory crypts and explain the situation to them. They can alter reality for a scroll of six more wishes (according to magical theory, the highest number of standard wishes a single scroll can hold is six).

His first priority is increasing his wisdom, followed by his other ability scores. He's incredibly smart and a fairly wise. It would be better to have more. Minor decisions he makes now could have major impacts in the future. To the memory crypts!

The memory crypts are a dark and quiet place. Rows of long storage containers are embedded into the walls. The number of containers marked 'empty' far exceeds the number of containers marked 'in use'. Mental pressure emanates from the containers which are in use.

The crypts hold people in stasis using quintessence, a psionic substance that inhibits the flow of time. It also inhibits the usage of psionic powers. Ennis is a wizard with no psionic talent and is thus unaffected by the mental pressure.

He removes the latch on one of the containers and slides it out of the wall.

The container holds a woman in a well-made outfit. She's sealed within a large amount of shimmering translucent silver substance.