The clutch release noise part made sense, but it sounds like the shop fixed it. What was your question about that? Did the shop put in your old throw-out bearing? That would be kinda silly. Then the 'clutch release' came loose? What's that? The release fork? Throw-out bearing? Or just the release cable?

Well, I suppose you got the MIL codes out of your shop manual, but you don't say what codes you got. That would help. I'm not surprised they have to do with the distributor, seeing how your rotor looked. Maybe the CYP, TDC or something else in the distributor is damaged.