May be a dumb question, but I can't figure out if these round metal plate pieces (where the bushing pieces sat).. if its apart of the car, or is it seized on, because I'm assuming it needs to come off but they would not budge.
A bit hard to tell due to the rust and since it was previously undercoated.

From looking at the parts diagram (upper strut mounting kit) I do not see that piece. It just shows a hallow tube running in-between where the stock strut slipped through.
Just making sure because I either have to try hammering out the middle piece, or the round circle plates?

I'm in the process of installing a 2" lift kit on my 3rd gen (springs and new struts).
Cheers

 

I think that is welded to the body. Is supposed to align the rubber bushing in the right spot for mounting the strut. Doesn't look like you have a "replacement" piece along with your strut kit. Leave it where it it.

 

I figured that was the case

Just have to try and remove the center piece it appears but it's seized in place. The diameter of the new strut is larger so can't be installed till I remove it

 

I'm not 100% sure, but there might be a metal insert inside of that guide that can be removed. That will allow you to use larger strut. See if you can use a punch to remove it if it didn't came out with the old strut and bushing.
It does show up as a replaceable part in the Gen3 parts diagram - Part No MR418161. Take a look at this photo for the rear OEM strut assembly, it is shown as a wearable/replaceable part there too.
Also, if you are using Old Man Emu strut, call/email them and ask about that. They'll know for sure if you need to remove any additional metal bushing from the strut tower.