There are rules that allow adding/improving a Fly speed and Spell-Like Abilities

The rules for Construct crafting include rules for modification.

Homunculi begin with a Fly speed, but it can be improved for "having wings":

Constructs with a fly speed can improve these speeds by 10 feet, up to a total speed equal to double the original speed, at a cost of 4,000 gp per 10-foot improvement.

And Homunculi in partucular can gain 1/day Spell-Like Abilities:

Spell-Like Ability: By incorporating 10 potions of the same spell in the homunculus’s creation, a crafter can imbue the homunculus with the power to use that spell once per day as a spell-like ability. Price: Total cost of the potions used.

Unfortunately, no Construct rules allow for gaining a prehensile appendage, such as a tongue.

Your (former) player probably wants Fleshwarper.

There is no example Fleshgraft for a prehensile appendage, but it does provide the structure for accomplishing it and gives the player the mechanical means to do so. They will have to work out with the new GM an appropriate statblock. Bonus: it's based on Craft (Alchemy).

Notes:

• They can consider Wings of Darkness if they prefer this method.
• Grasping Tendril is probably the best starting place for the tongue.

There are rules that allow adding/improving a Fly speed and Spell-Like Abilities

The rules for Construct crafting include rules for modification.

Homunculi begin with a Fly speed, but it can be improved for "having wings":

Constructs with a fly speed can improve these speeds by 10 feet, up to a total speed equal to double the original speed, at a cost of 4,000 gp per 10-foot improvement.

And Homunculi in partucular can gain 1/day Spell-Like Abilities:

Spell-Like Ability: By incorporating 10 potions of the same spell in the homunculus’s creation, a crafter can imbue the homunculus with the power to use that spell once per day as a spell-like ability. Price: Total cost of the potions used.

Unfortunately, no Construct rules allow for gaining a prehensile appendage, such as a tongue.

Your (former) player probably wants Fleshwarper.

There is no example Fleshgraft for a prehensile tongue, but it does provide the structure for accomplishing it and gives the player the mechanical means to do so. They will have to work out with the new GM an appropriate statblock. Bonus: it's based on Craft (Alchemy) and seems to cannonize what the player was already doing.

Notes:

• They can consider Wings of Darkness if they prefer this method.
• Grasping Tendril is probably the best starting place for the tongue.

There are rules that allow adding/improving a Fly speed and Spell-Like Abilities

The rules for Construct crafting include rules for modification.

Homunculi begin with a Fly speed, but it can be improved for "having wings":

Constructs with a fly speed can improve these speeds by 10 feet, up to a total speed equal to double the original speed, at a cost of 4,000 gp per 10-foot improvement.

And Homunculi in partucular can gain 1/day Spell-Like Abilities:

Spell-Like Ability: By incorporating 10 potions of the same spell in the homunculus’s creation, a crafter can imbue the homunculus with the power to use that spell once per day as a spell-like ability. Price: Total cost of the potions used.

Unfortunately, no Construct rules allow for gaining a prehensile appendage, such as a tongue.

Your (former) player probably wants Fleshwarper.

There is no example Fleshgraft for a prehensile appendage, but it does provide the structure for accomplishing it and gives the player the mechanical means to do so. They will have to work out with the new GM an appropriate statblock. Bonus: it's based on Craft (Alchemy).

There are rules that allow adding/improving a Fly speed and Spell-Like Abilities

The rules for Construct crafting include rules for modification.

Homunculi begin with a Fly speed, but it can be improved for "having wings":

Constructs with a fly speed can improve these speeds by 10 feet, up to a total speed equal to double the original speed, at a cost of 4,000 gp per 10-foot improvement.

And Homunculi in partucular can gain 1/day Spell-Like Abilities:

Spell-Like Ability: By incorporating 10 potions of the same spell in the homunculus’s creation, a crafter can imbue the homunculus with the power to use that spell once per day as a spell-like ability. Price: Total cost of the potions used.

Unfortunately, no Construct rules allow for gaining a prehensile appendage, such as a tongue.

Your (former) player probably wants Fleshwarper.

There is no example Fleshgraft for a prehensile appendage, but it does provide the structure for accomplishing it and gives the player the mechanical means to do so. They will have to work out with the new GM an appropriate statblock. Bonus: it's based on Craft (Alchemy).

Notes:

• They can consider Wings of Darkness if they prefer this method.
• Grasping Tendril is probably the best starting place for the tongue.