You DO NOT bolt the torque converter to the flex plate before installation. Put the converter on the trans, push in on it hard and turn it at the same time. You will hear two clicks as the converter goes back as it engages the pump and gearing. If you do not do this, you will destroy the trans. When correctly in place, the front of the converter WILL NOT be in front of the trans bell housing.
To install the engine, you have to jack up the front of the trans. I don't know what you are using to lift the engine, but the engine should have a tilt to the rear. You lower the engine slowly jockeying it into place and aligning the trans.
With an automatic, connecting the two together isn't very hard. Take your time, and be patient.
shady