The cover gaskets are in the overhaul gasket set they listed.
The spark plug grommets are built into the boot on the spark plug wires.
There is also a third valve cover or rocker cover "gasket" which is the big black thing running down the center of the two covers... the plug wires reach between it. It is advisable to replace it as it helps keep oil away from the spark plugs if the other cover seals are leaking and it helps keep dirt from dropping down in there as well. It is not as inexpensive as the seals for the two covers though. And yes, there are two rocker cover seals, one for each side.
I just want to know how the Toyota shop diagnosed the blown head gasket, really. It's not a given they used any of the methods I mentioned, there are a few tests which will indicate the HG or not... but for a firm diagnosis more than one needs to be employed.
There is only one place where sealant is used... use a GOOD sealant for the job, either Toyota's recommended FIPG (form in place gasket) material or "The Right Stuff" if it is available in your region or an equivalent.
If you look
here you'll find an exploded view of the cylinder head and components. Toyota calls the covers we've been talking about the #1, #2 and #2 cylinder head covers. On that same page is the torque specification for each srcew and bolt... be sure to follow those values when putting everything back together; These engines are VERY tempermental if things are over or under tightened... this is very easy with a decent torque wrench and the folks at the parts store should be happy and able to show you what the value on the page that you need to look at is and how to use the wrench.
Tools: Socket wrench, 12mm and 10mm sockets, one socket extension (I think 12in/30cm or so will do), torque wrench, phillips screwdriver, 14mm hex socket (for the #3 cover), a couple towels.
The first picture
here shows where to put the sealant. Make sure there is absolutely no oil on the surface when you put the sealant on. Do NOT use sealant anywhere else.
When you reinstall the rocker covers you may tighten them with a regular screwdriver just hand tight; most torque wrenches of higher values like you want for the rest of the job either do not go that low or they are too inaccurate that low. So, unless you want to buy second torque wrench for the appropriate range just get them good an hand tight. I recommend using blue thread sealant (non-permanent type; they can get it for you at the parts store) on the screws and replacing the 12 grommets/rubber backed metal washers with new ones from Toyota is a good idea.