Well to do a proper analysis it is not allowed to have interferences between parts.
You can use (bolt)connectors instead of modeled bolts to make it easier.
Seems like (without seeing the geometry) you could model the threaded inserts as simple tubes and globally bond them. I don't recommend using "bolted connections" as the way they are implemented in SW leaves a lot to be desired and will run up your computation time considerably.
Try simple geometry without any threads first and see if it makes sense.