I'm no expert but, I believe the deeper pan would only require more fluid to achieve the proper level of fluid above the filter. I'm not sure how far the seal should be up the filter tube, sorry I can't help you there.
When installing the torque convertor, slide it all the way in until it bottoms out, it may require a little turning to engage the pump. Once it's engaged, if you turn the convertor you will hear the pump rotate. Then once you install the trans, slide the convertor up the the flywheel, and bolt up. That should do it. If still no gears, install a pressure gauge to the main line pressure port on the drivers side above the gear selector and see what you've got.