Intake Manifold Maintenance

Okay, the engine and transmission are out of my car (I guess this means it's really my car). It will get a new clutch, flapper, those tensioner thingies that (hopefully) save the engine (I cannot afford the upgrade), and a few other things. As long as I am at it:

The rubber connections between the air box and the intake manifold are pretty bulgy, like old radiator hoses, and soft as well. My question: should these be replaced as long as it is so convenience? It looks like the whole fuel/air handling system can come of easy now. Further, should I replace any gaskets at the engine-end of the intake manifold (this seems to be bolted to the red plastic air-handling shroud), or woudl it make more sense to just check them for proper tightness?

There is a VERY subtle surging in this car (not unusual for CIS cars in my experience) that I am not worried about, but as long as the engine is out, I would like to make SURE that air is not getting into the engine without goung past the sir flow sensor.

By the way, your engine removal tech article was VERY helpful