I might have answers for you in regards to a couple of glitches outlined in the Changelog.
Black lines from a distance is almost universally an issue with mipmapping. Mipmaps are downscaled textures used to save memory and render costs when viewing objects from a distance. They are generated automatically by downsizing the texture by powers of 2. This blurs the texture and if the polygons are mapped very tightly to it, the surrounding pixels (which in your case are probably black or transparent) will bleed inside. This can easily be fixed by expanding texture island edges past the polygons that they're mapped to. During my own playtests I didn't really find the black lines distracting, they sort of fit the low-poly look of the game.
Phasing through walls can be remedied by making the box colliders on the walls really big, or playing around with the Character Controller or Rigidbody on the player character (whichever you're using here, feels like a Character Controller to me). Making the colliders really big is a pretty good solution since most of your game is blocky, so the colliders can be expanded well past the actual wall. The other way is to change the collision detection on the player to "ContinuousDynamic" and play around with the skin width values if you're using a Character Controller. "ContinuousDynamic" detection is very costly, so only use it on the player character. If after these changes the player can still see through walls, change the camera clipping planes.
Coin locations not saving between scene loads can be remedied by any of the methods mentioned here: https://stackoverflow.com/questions/32306704/how-to-pass-data-between-scenes-in-unity
Also if this is your first stab at Unity and 3D in general I'm very impressed. This is nothing close to my own first Unity project.