UIM, what are these ports for?
 

First of all I have a JDM car so I know my UIM is slightly different. I purchased a US UIM from a forum user because it was polished and I was too lazy/cheap to polish my own.

Now that I have mine off and I can compare them I see the original owner has done a bit of work to it. Like removing the secondary throttle plus some other things.........

My JDM has two more nipples on it then the US one. It looks like he cut them off and capped them. What are these for?

I should have mentioned a couple of things.....

1) my car is emissions legal
2) my car is running sequential

The one nipple goes to another check valve. But again I do not know what that check valve does or how it would impact 1, or 2.

Thanks for looking and any input would be appreciated.

Just look at the vacuum diagram:

http://www.fd3s.net/vacuum_hose_diagram2.jpg

Perhaps my question should have been is how can I add back on the removed nipples?

To add them back, you'll have to drill the holes back out and add the appropriate sized nipple.