He did. He also fought and lost to Vegeta. We should be very familiar with Shadow's abilities by now, and unless he's had a new release lately I don't know about, the stats we've seem them use is no where near close enough to win.
No, he scales to normal Sonic. Flash fought Archie Comics Sonic. Those are two completely different creatures. Normal Sonic loses to Mario.
Numbered for convivence
1. True
2. True
3. False. Unless Shadow can permanently stop time, Ryuko will just regenerate when the time stop err stops. Even if he tore it out, and threw it to the moon, it would be yanked back into Ryuko's body with no real negative side effect beyond momentary discomfort. He'd need to completely destroy it on a molecular level, and Ryuko+Sangetz is simply more durable than pretty much anything we see in the Sonic Universe. And even that might not work because Ryuko runs on ridiculousness. It would be entirely in character for her to walk around with a hole in her chest, pull out someone else's heart and use that as her own. I mean, in the end, they didn't actually kill the BBEG of Kill la Kill. They did something so stupid that the BBEG committed suicide rather than exist in a universe where that actually worked.
And I'm not convinced Shadow can even do that in the first place. We've seen what feats he gets, he's been in DB three times now. If he doesn't have the power to kill Vegeta, or the speed to blitz Mewtwo, he won't be able to beat Ryuko either.