Very new to this hobby and have a few questions

So I'm planning on adding, plants, shrimp and snails to my jar but due to bad timing I was able to retrieve pond water and mud but no plants.

it's been about a week of the jar sitting like this and I'm seeing some cool worm looking guys sticking out of the soil but I'm going to have to drain the water to add the plants. what's the best way of going about this?

Secondly, is are the pebbles I put on top of the mud too large? I'm assuming it's fine but a lot of people here use much finer gravel that I wasn't able to find locally. Lastly does the water seem fine for plant growth/shrimp and snail habitation? obviously I'll be letting it sit for a month or so before adding animal life but I thought it would have cleared up somewhat more by now and I just want to make sure I don't harm anything. Thanks everyone!