Do I need to use gasket sealer with the port gaskets?
No, but its not a bad idea. I do.
Any other seals under there that I don't know about - I've already got all the hoses and the seals for the oil seperatro.
There is a seal under the top of the AOS cover that is between the cover and the body of the AOS. I wouldn't worry about it though.
Is this the time that I should also be replacing my oil cooler seals?
Never a bad idea, but not related to the intake manifold. However, it is an excellent idea if the headers are ever off the car.
Anything else that I may need to do well the manifold is off?
Will be a little easier to check/clean your DME grounds (Procedure from Tom's site)
Might also want to replace your fuel injector seals if this hasn't been done recently.