Evo 9 MR flywheel
 

Was just wondering if the flywheel from a 5 speed 8/9 would fit an 6 speed Evo 9 mr?

Yes, they are exactly the same. I had a flywheel machine shop cross reference lookup to make sure before i had them resurface the old flywheel from my old 5 spd to put into my 6 spd. It bolted right on with no problems and everything matched up the same.

The only thing different is the clutch disk because the input shaft splines are different.

Yup, they are cross compatible. I took my entire ACT 6 puck sprung clutch kit with their flywheel off of my 5 speed and it was a direct bolt on fitment to my 6 speed.