Answers are:
1. Don't undo those ones, undo the other ones. Leave the rubber donut attached to the tailshaft.
2. Through the starter motor hole.
3. Undo that bolt for the black bracket on the trans. From there you can lever the lines out from the trans. Move them to the side, no need to undo the heat exchanger side to remove the trans. Those quick connects are easy to undo though, spray them with WD-40 and move them back and forth a few times, then you can undo them by hand. There's probably a tool for it, I know you can get quick connect tools for fuel lines etc. Google is your friend