Events broken in SoulSilver Save

[JunieVargus]

Hello, this is my first ever Pokemon game and I've noticed an issue ever since I finished the Johto region. Immediately after finishing the game, I noticed something was off, Professor Elm was supposed to give me a ticket to get on the boat to Kanto, but he never did. He acted as though he had already given it to me. This is when I learned about PKHex and was able to give myself the ticket. After arriving in Kanto, I was soon given a Clefairy doll for a girl I haven't met before. I soon found the girl and was given the ticket to the train, which I thought nothing of at the time. Now I'm at the point where I've arrived at Misty's gym. She isn't there. An NPC mentions something about the power plant. When I get to the Power Plant, they all thank me and say the power plant is already fixed. I have no idea what's going on but I think I might be unable to progress. I was wondering, do I now have to edit event flags in PKhex? Because I'm afraid I might ruin things further if I try due to me being unknowledgeable. Any help is appreciated, thank you.

A few side notes: I'm playing on a DSi with a flashcart. The only cheats I've used are to disable encounters and a toggle for running.