7th suggestion: Player position reset in Escape menu, along with crystal position resets. The player position reset would work like you woul expect, teleporting the player back to whichever shop they use. The crystal position reset would reset the crystals to their default positions. The only exception to the crystal reset is if the crystal has been brought into either shop at any time during the game. Resetting the crystal positions will move any crystal that meets the previous requirement to the counter of whatever shop is currently used (1. floating in the air, about dagger height or more above the counter, and 2. each one having their own designated position above the counter).
8th suggestion: Ore Vein Tracker. This would have an arrow floating a bit over the ground (pointing to the vein) and/or a highlight around the vein, similar to the way mentioned in the 3rd suggestion (item highlight). You would go into a menu (either button activated or in an inventory slot) and select a type of ore. Any vein of that ore type will have an arrow and/or highlight until all of its ore has been mined. The arrow (if you use it) would grow/shrink depending on the distance from the vein, with a shorter distance meaning a bigger arrow.
I might have more suggestions, but I can't think of any more right now.
(Edit) 9th suggestion: Fold-out platform on horse cart, that you can click to fold/unfold. Ideal for standing on, this would make accessing items in the cart so much easier. It's hard enough to try to climb up on the wheels and get inside, so having a platform to stand on would be cool.