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I'm closing in on the end of my Giratina Strikes Back LP, and I'm glad to see that there's another interesting hack by the same creator. Not only that, but this one sounds like a lot of fun, especially considering that you play as Team Rocket
The Porygon might not have been coded to evolve at Lv.40 or it's just glitched but you can always try giving it a Shiny/Dusk Stone. As for Magmar, it most likely requires a Fire Stone to evolve