Its been a few years but I remember some guys having issues with the TORS. The issue is usually solved by adjusting the throttle cable or if the speedo side bearing is shot it can mess with it as well. TORS is easy to bypass, but I also thought it limited RPMs below clutch engagement to prevent a run away.
If it was running fine with weird RPM fluctuations I'd dig into the clutches first and look for worn out parts and broken springs, but the miss is weird, especially with no codes being thrown.
If it was me, I'd put electric grease on every connector you can find, then bypass the TORS, then start looking at things like the coils, voltage output, ECM, and fuel pump.