The GFX thing happened to me, I enabled Vsync and it fixed it. Though the audio can be choppy at times, but it's doing a lot better with Vsync on. It doesn't bother me much.
As for the .ips problem you need to use Lunar IPS, a program you use to patch the original Pokemon Ruby Rom (and roms in general). There's a tutorial here somewhere for IPS files I'm sure of it, use the search bar on the forum to your advantage.