Please please please do not add these enhancements to a "stage 3" that requires Stage 2 to be completed. Stage 2 is fine as a prestige trial with no huge benefit. The trials are completely unrealistic but also truly optional. If you add the proposed exclusive pets spells and abilities to a 3rd stage then you take that away.Additional planned features, such as equipment-specific magic spells and pets, have been postponed to allow for more thorough testing concerning attributes, the number of potential users and the process by which to obtain them. One consideration is whether to implement such features as another stage of the above upgrades, or to apply them to a different set of equipment. Also under deliberation is whether to limit the availability of such equipment or make it relatively simple to obtain.
Any major functionality of ultimate weapons should be obtained from reasonable trials that a majority of PCs who have put in the work to get up to level 99 weapons will be able to obtain.
I believe a good option for these trials would be to require an objective that can only be completed with the 99 weapon but instead of changing the stats on the weapon once the trial was completed the player would then have access to the new pet, spell, ability. That way you don't run into the problem of reorganizing magian trials or having to create a split path.
An Example would be:
Required Item: Guttler
Defeat Nidhogg 10 times with Guttler equipped.
Reward Item: (Key item) Wyrm Trap - Allows the master of Guttler to Call it's favorite familiar. - Uses Bloodthirsty Broth to Call Flimblepim Flappidyfling or something with a less ridiculous name
or
Required Item: Mandau
Perform Mercy Stroke 2000 times in Dynamis
Reward Item: (Key item) Assassins codex - Instructions for targeting your foes most vulnerable points using your Mandau. - Increases critical hit rate by 5% with mandau equipped.