You don't need to replace the bottom plate unless it's damaged. I would replace any worn parts but you may need some new parts in hand to compare to see if they need replacing.
Can't help you with the closed shackles.
I don't think you really need to do that. I have put over 2500 miles on my CJ3A in Utah on the trails the last two months and some of it was extremely rough dugways over large rocks with me showing it no mercy. I have broke nothing and put my Jeep through a lot of rough abuse.
The only thing I plan, other than checking everything real good, is to install a Lock Rite in the rear axle.
