After a long weekend of much water and mud in the jeep, it's time for the carpet to come out. Starting taking out the passenger side last night, here are some pictures. I believe I see in the rear back seat, under the silver lining, there is a drain plug there. Is there another I am missing???

 

There are a lot of drain plugs in the XJs. Cant miss them once all the carpet is out. Both sides of the front and rear floor pans, and a few behind the back seat.

 

Where can I buy the kit?

 

What kit?

 

The plugs... Seems there's 1" ones and 3" ones.
Do I have to buy them separate?

 

It's just a plastic "Cap plug" visible in your picture. Just pry it out with a blunt prybar and either put it back in place with a rubber mallet or leave them out.

 

X2, you can just put the stock plugs back in, or leave them out. I left all mine out, it doesn't really matter either way.