My upper intake has 2 hose ports on the bottom that are used to cool the throttle body i guess. They are Aluminum and the are cracked and spray coolant everywhere. Is it possible to just cap the off and bypass it with some heater hose without damaging anything?

I blocked off my passages a few years back. No problems with it.

ok so what exactly do i need to do? Can I just bend some heater hose to fit both ends of the pipe that the coolant comes from?

Not sure how yours is set up, can you post a picture? Mine comes up threw the LIM and I simply blocked off the passages.

I've done the same. I assume you have a 3100? I just ran some hose from one, right under the throttle body and around to the other.