OK, there are a lot of questions on this thread. Let's start with the easy one, tube seals (otherwise known as valve cover grommets).
The valve cover grommets have a marking, or tab, on the outside diameter. These are primarily there to help in positioning them properly when reusing them to reduce the potential of oil leakage. Besides ensuring that the #1 grommet goes in the #1 position on the valve cover, there is a standard by which the tabs are positioned so the grommets are also in the proper rotated position on the spark plug tubes to help reduce chances of oil leakage when reused. These tabs should be facing the camshaft sprocket (timing belt) end of the engine, and should be within +/- 15 deg. of facing perfectly towards the front, or camshaft end, of the engine. This way, when you remove the grommets in the future, and make sure you reinstall the grommets in the right spark plug tubes, you can also get their rotation correct again to minimize oil leakage.
Now you said you replaced gaskets & seals. If you replaced these 4 grommets, the new ones won't leak if you didn't align these tabs properly, but you probably won't be able to reuse them again if you need to take the valve cover off in the near future either.
Now let's focus on your main issue, engine shaking. Did this issue cause you to replace the valve cover gasket/seals, spark plugs and wires, or did this issue start after you put these new items in?
You also said there was some oil in the bottom of a spark plug tube, which you cleaned up, but the plug was fouled. I'm assuming this happened before you changed the gaskets/seals, spark plugs and wires? Note that it is most likely a valve cover grommet that was leaking oil that got the oil inside the spark plug tube...you don't remove a spark plug tube from the cylinder head to seal it, as they are pressed in and should not be removed.
Lastly, the spark plug wires: I'm thinking on your engine, you have the round apron boots at the top of the spark plug wires to form a seal on the top of the valve cover, right? Later models (1992 on up) used square aprons, so you wouldn't have an option but to install them one way. If round aprons, there isn't a specific way to face the wires, but typically they face towards the distributor and towards the front of the car, angled at about 45 deg. or so. But this isn't critical. New spark plug wires should click, or you should feel them latching onto the spark plugs. If the plug wires are new, and you didn't get them to latch onto the spark plugs properly, I would return them for a different set (if new, the place you got them should exchange them for you).
I might be able to help you more once you address each question asked within this reply.