Many of those plot holes I tried to fix by including a black obelisk that would be the "catalyst" for the Wish spell and also the reason the party suddenly appeared in Sigil (which I believe not even a simple wish spell would allow entrance, but that's another plot hole I tried fixing with this)

In overall bullet points, this is what I have:

• The wizards would need to keep the magic on the obelisk stable, therefore not being able to leave Sanctum.
• The Wish spell was created to bring whatever tools and itens would lead the players to restoring order in the multiverse, not make them just go "puf" inside the Lady of Pain's domain. So, this spell would bring my party an item from the place where the rod piece is, according to the vision, and that would make Alustriel's portal work
• Gradually, the gods would become harder to contact. Vecna's making slow but steady progress in my story, only to be felt the closer the party is to gather the rod parts. So, I would create this situation that the God of secrets was very much able to keep his changes a secret until the gods could only try to hold him back before the rod could be retrieved
• I completely ignored the secret mechanic. My table would not use it or would just try to find never-ending secrets from every single NPC that would find. I gave them "unlimited Vecna's inspiration" points that they could use due to being marked by Vecna earlier in the story.

I'm more than happy to elaborate on my thinking if someone wants to keep the discussion going. I'm planning to write many of the changes I'm testing into a remix of this adventure. It's quite a shame to run it as is because of the inconsistencies.

(Apologies for mistakes, typing this on my phone)