Andy, glad you've got the new liner! I'll answer the questions by #.
1 - I would pour bleach directly on any effected area and go ~ 1' past the visible stuff
2- I suppose that you could patch with sand, but it won't be a lasting patch. I think you'd be better off using some cement (and either sand or vermiculite as the aggregate).
3- We are mere humans and as such cannot stop the forces of nature - you've done about all you can for the roots. As a practical matter, I've never seen a root under a liner that was large enough to harm the liner (I think the pressure of the water in the pool tends to keep the roots 'at bay'.)
4- You are dealing with 2 different types of gaskets. The returns have a rubber gasket that should be behind the liner. The skimmers, lights and main drain have fiber (~cardboard) gaskets and there should be 2 for each one - they go behind and above the liner (the liner is sandwiched between the gaskets). For the ones that need to go under the liner, you can secure them with duct tape or spray adhesive before dropping the liner.
If you have any other questions on installing the liner, please feel free to ask! I've dropped well over 1000 liners (and then I picked them back up and installed them in the pools) and may be able to give you a tip or 'trick' that would make it easier
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