Wish we could see a picture of how you have things ran. Should have 3 ports connected if you're deleting the heater core and throttle body connections.
The large one on the intake manifold is the return from the head, this should loop out and connect to both the ports behind the thermostat housing. Basically should have a T in that loop. Then you'd just cap off the lines that are supposed to go to the throttle body (or loop those together also).
Hopefully you still have some of the hard pipes around, easiest way is to cut those as needed.
Here's a picture I found in another thread after a quick search, should give you an idea to compare your setup with.
https://zilvia.net/f/showthread.php?t=644900