could use some suggestions on a fix... I've got a 176 (manual) to TF 727(auto) swap going on in my cj7. When at Idle and higher RPM I get a vibration like the engine is missing on a cylinder or two. This vibration is happening while at idle or rpm so the problem is not associated with driving. I believe the vibration is possibly associated with the flex plate to torque converter. Does anyone know if there is a specific torquing sequence to install the torque converter to flex plate bolts? I think I just tightened them to the haynes ft lb.

yes, the flex plate is the unbalanced 258.

any other suggestions on what could cause this type of vibration

Depending on where your torque converter came from, it could have weights on the front side of it somewhere between where it bolts to the flexplate. If so, remove them. Some Mopar engines are externally balanced and require the weights, I think some AMCs use weights too. Like I say though, depends on what the converter was intended for.
Travis..