The event doesn't work on me now. I already visited Route 42 but Lyra was not appearing. Maybe I should give up on this hack now since there is no way of getting Whirlpool.
Two more ways that would allow you to continue. Shellder learns Whirpool at Lv 40. In case you haven't caught it already, you can find one on Whirl Islands (Ha! That won't help.) or fish one at Olivine Harbor or Cherrygrove Bay with the Good Rod. It'll be Lv 20 though, so you'll have to train it a bit. Or maybe you could try to get one from Wonder Trade. It seems you'll need to trade a Pokemon up to Lv 33 to have a chance to receive a Shellder.
Or you could use one of the following GameShark codes:
91FAEADC - Makes Whirpool the 1st move of the 1st Pokemon in your party.
9101A6D8 - Gives HM06 to the TM/HM pocket in your bag.
I tested them, and they both work. I use VBA, however, and don't know how MyOldBoy works when entering codes, but I don't think they wouldn't work on it as well.
Now, reporting for some more fixes. Very minor thing, but the guy that gives you TM10 Hidden Power at Lake of Rage says both its power and type depend on the Pokemon using it, but now Hidden Power has a fixed base power, so I guess you should correct that.
While battling Clair, I noticed a flaw in the AI, in which she was constantly trying to inflict paralysis on my Electric type Pokemon despite Electrics being immune to it now. I don't know how simple it would be to prevent the AI to use innefective moves, but considering how you fixed the Baton Pass abuse I figure it should be doable.
As the Slowpoke evolution issue was reported, I decided to check if there were more victims of this bug. Turns out it happens to Eevee as well. When trying to evolve it to Leafeon/Glaceon at the proper locations, if Eevee has enough happiness it will evolve to Espeon/Umbreon instead. This isn't as bad as Slowpoke's case, since its possible to lower happiness, but Leafeon/Glaceon should have a priority over Espeon/Umbreon.
Lastly, I noticed some of the new music added - specifically, Yellow Forest and XY Gym Leader Battle (vs Valerie) - play at a lower volume than usual. You'll be able to notice it when the music is interrupted for a brief moment (when you get an item or level up, for exemple), as it resumes it will play at the regular volume. At first I thought maybe I was unhearing it, but it seems clear to me now after I could hear it from another music you added. It's completely harmless, I know, but it was kinda bugging me a bit.