People have no idea how badly that motorcycle accident messed Mir up. At first they were saying he may never walk again without a crutch or at least a noticeable limp. Even when he came back, he did it way too soon and looked like garbage vs Pe De Pano, Christison, and Vera. He never got back his explosion or flexibility either. Look at how fluid he was on the mat prior to the accident, then after. There's no comparison.
But he figured out how to adapt to his new limitations and ended up having a big resurgence and a hell of a career. There is no telling how good he could have been if not for that accident. That said, he'd have needed some sort of wake up call because he admittedly didn't take things seriously way back then and just assumed he'd sub everyone based on talent. Didn't train hard, etc.
To answer the question, as has been said Frank never really had a "prime". Maybe the best version of him was when he KO'd Nog the first time? Nog had staph, but Mir really lit him up. The fight didn't take long so it's hard to know how "peak" that Mir was. Stipe is a bad stylistic matchup though. Faster hands (though I think Mir hits harder), better footwork, good TDD. I'd give the best version of Mir a decent chance for sure, but gotta favor Stipe. And Mir is literally my favorite fighter ever.