I am putting my motor back together and when I put the LIM back on I noticed there is two orings that sit in the rotor housing sections. I understand coolant flows through there. Why is the o-ring there as well as the gasket for the lim?

When doing the TB mod. If I want to keep the thermowax I just have to cap the hole where the little vacuum valve was at correct? It is circled in the below image

 

You don't have to cap the spot where the thermovalve was. No coolant flows out of there, the thermovalve works just by the heat transfer through the metal.

The o-ring in the coolant passage to the LIM is there so water doesn't spray everywhere. The paper gasket is more for sealing the intake runners since there aren't bolts directly next to the coolant passage. Leaving the o-ring out risks having coolant leak into the intake.

 

gotcha. yeah when i pulled the manifold off there was the two orings but only one hole in the LIM.

So when I pull the secondary throttle plates I just need to cap the "front" side of the tb and not do anything where the thermowax is?

 

You don't need to do anything on the thermowax side, but I still filled the hole with RTV just in case. It's got a plastic spacer that should be fine though.