Took out my HVAC and I want to remove the hard lines that run between the upper and lower intake. There is the ECT sensor there so I will probably need to run an adapter to put it where the line come out of the intake. The other end goes to the waterpump and I am guessing I could just block that off? Am I correct? Or does it need to run into the intake. I know about the EGR coolant lines, I'm not worried about that.

You just need to run 2 hoses like they did back in "the day". One reason I can see to get rid of the hard lines is to help clean up that side of the engine a bit. It's a mess on that side compared to the other side of the engine.