Look online for liner and compare liner costs to yours locally. As backwards as it seems buy the liner last after you have everything else 100% planned out. Planning now will save a ton of time and money in rebuilding later.
No experience with that pump, but you can get a nice external or two for similar or less money that will last a long time and use less energy. The pump should be picked after the filter and plumbing plan to decide on how much head and flow you need.
You can mod a pool skimmer for very cheap, Around $50.
Think bottom drain.
A few things to search online, use the word "koi" with "sand gravel" "settlement" "Fluidized" "skimmer" and "bottom drain"
Keep the details coming, its a lot at once, but the info is out there and its much easier to plan right than to get frustrated for a few seasons, replan and rebuild