So, my JDM engine arrived. It's extremely clean. I'm currently ordering parts...and when I was looking at the valve covers I noticed what looks like a semi-clear silicone that was used to help seal up the valve covers. They don't look like they are leaking at all. What would you do? Change them or leave them?

Those plugs get sealant from the factory but that looks sloppier than most. 

At this age it’s not a bad idea to install new valve cover gaskets and spark plugs so you don’t have to think about it again for a 100k miles. Address those while it’s out. 

That being said they aren’t hard to do in the vehicle if you don’t want to. 

Definitely do the spark plugs now. They’re annoying in the vehicle and the stock plugs are so good they last a loooomg time. 100k easily.

Valve covers can go either way. Would you rather have down time now or later?  How frugal are you. How annoyed will you be if you have to do them later…lots of variables.  

 If you decide to skip, check the bolts. I found some were barely finger tight, but,don't over-torque the VC bolts . The value is quite low and they have been known to snap.

It seems it's a good thing I ordered the gaskets with my new hoses then. I was leaning toward replacing them.

The next question is whether I should mess with the lower oil pan...It doesn't seem to be leaking as there is definitely oil in the motor at the moment. It doesn't seem to be dented or bent but I will do a closer inspection in a few days. I'm leaning toward leaving it alone if it's not leaking and doesn't look damaged. I can always change it later.

Also, does anyone know if these are the same mounts as the outback has? I'd like to use the newer ones if possible.

i have no idea on the mounts, but i would seriously change that oil pan drain plug - that thing looks nasty.. somebody used the wrong wrench on it or something..