Replacing liner?

After 12 years it is time to replace my liner. I have a few questions
before I do so I don't screw this up.

When I first built the pond I didn't make the bottom flat. ) It is 12
foot wide by 20 foot long by 3 foot deep). This I later found to be
a mistake. I corrected this by adding about 10 inches of gravel to
level it out. This has worked OK although it is not easy to keep
clean. What I want to do is fix this problem at the same time I
replace the liner. I want to install the new liner over the old one
and use the 10 inches of gravel to level things up. This brings me to
a few questions.

The original liner was a rubber material about 20ml thick. It has a
small leak somewhere well below the waterline. Is there a preferred
material I should use for a replacement?

If I leave the old liner in, should I make holes in the old liner to
prevent the new one from floating or just lay it on top? The pond is
elevated a bit above ground level and the soil is thick clay.

Should I use adhesive around the top to prevent water from getting
between the liners? If so, what type? Silicone?

I have some rocks that have always had a tendency to fall in. Using
expanding foam may be a great solution for this. If this breaks down
over the years are there issues with toxins?

Would you recommend adding a thin layer of gravel to the top of the
liner? I kind of like the look of river pebbles and it might help
keep water from getting under the liner.

Any other pointers would be appreciated. I have about 20 (6in)
goldfish and a bunch of bluegill that I plan to move into trash cans
during the process. I will keep the temperature as stable as possible
ad well aerated since the weather is supposed to be hot.