1969 Trunk Questions

Hi,
I am new to the forum, so hopefully this is posted in the correct thread.
I have had my 69 Eldorado, blk on blk, for 4 years now and it is time to fix up the trunk.
Has anybody undertaken this task before?
I had some moisture issues in the trunk so I tore out the trunk carpet today.
Turns out the rear quarter drains were plugged an there was a pool of water sitting in either side. I have cleared the drain holes and the water is now gone.
I have started scraping off the black adhesive in the trunk and have discovered some surface rust underneath.
Any suggestions for a good rust treatment?
Any ideas where I can buy the replacement cardboard sections that cover the back of the rear seat and quarter panels in the trunk.
Should I restore to match the original carpet or just do new paint and a thorough clean up in the trunk?
Thanks,
Luke