From your description it is confusing about what is ‘bent’. Is this something you see? Can you post a picture of it?
When not assembled, off the car, slide the companion flange onto the shaft. It should slide on all the way without resistance.
The parts that fit inside the bearings is where there is an interference fit.
Using anti seize on the splined portion is a good idea on assembly. It will aid disassembly later on.
Finding a vibration can be difficult. As Mark mentioned, different parts of the drivetrain rotate at different speeds, and understanding this can help locate the source of the vibrations.
You mentioned vibrations in the steering wheel. That suggests the vibrations are coming from the front of the car, not the rear.
If you feel the vibrations in the seat, that suggests the vibrations are coming from the rear of the car.
If you suspect the companion flange is bent, use a dial indicator and check for runout. It is an easy check, and the FSM should have a spec for it.
Also check the runout on your wheels, halfshafts, driveshaft, differential pinion and output flanges.
Be sure to closely examine the tires too, looking for damage, shifted belts or unusual bumps in the tread.
Be sure the tires are properly inflated.