Well, first of all, I doubt very much that your noise continues past 7000RPM. I don't know whether the rev limiter cuts the engine at 6500 or 7000, but it's one of the two. Mine shifts at 6500 at WOT.
I doubt very much that your transmission issues caused damage to your flywheel, but then I can't very well explain why I think that. My wife's Legacy has a very, very long 2-3 shift (especially in the cold) - it has since we picked it up last summer. It has not gotten better or worse, it just stays the same with no sign of giving out permanently.
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