I recently did a top end rebuild on a 5vz. Your list is pretty good, I'd suggest using the aisin kit for the timingbelt/waterpump as they're the oem, it will also come with koyo/nsk/ntn idlers etc. The only thing I'd add to it is make sure you reseal the half moons when you take the valve covers off, and use a good quality fipg like permatex the right stuff for the half moons as well as the oil pan.
As for that weird shaped piece with the foam around it, its just a cover plate to stop water and debris from getting into the valley under the intake manifold. Theres no oil or anything that goes through that area or anything like on a pushrod engine, so its not really critical that its perfectly sealed, its just there to prevent mouse nests and other annoyances as its just an open void other than a couple small (coolant I think) pipes. The foam usually is shrekt because of the exhaust crossover pipe that runs behind the block is very close to it.
Don't worry about replacing the oil pump, though it might be a decent idea to take it off and reseal it if you're tearing the front and oil pan off the engine anyways. Its just FIPG on the back side, and maybe an O ring iirc, and you'll need a new paper gasket for the oil pickup.
I'd resist the urge to do the head gaskets unless there are signs they are bad which is unlikely. The 5vz uses a MLS gasket and torque to yield head bolts, so if you take them off you're likely going to have resurface the heads and replace the bolts. I found this out the hard way when I did my rebuild, turns out someone replaced the head gaskets at some point using composite gaskets as a cheap fix. So when the new gaskets arrived and they were MLS I ended up spending the better part of two days flattening and resurfacing the heads using a pane of glass, sprayglue, and sandpaper.
