Pond liner is superior over anything else, if you can afford it. Other tipes of lining like shower curtains work great but you have to replace them eventually. Pond liner is indestructible. It lasts forever
It's pretty common for a tortoise to grow rapidly when it gets better nutrition. If it wasn't taken care of properly before it's normal for the tortoise to use it for growth.
Welcome to the forum. Could you post pictures of your enclosure? It could help everyone around here to help you make any improvements still needed. You sound like a caring person and we all want to help you. You've already received wonderful advice but pictures say a thousand words.
Just leave it in the enclosure. Don't get worried if it gets dirty, they like it more when "seasoned". If you're worried about your tort not getting enough calcium you could scrape some onto the food.
I'm also a bigger fan of tortoises. I've had turtles for years but the day I got Marley I knew he's the only animal I want to spend my life with. This might seem like over exaggerating but hey, "he's" probably going to outlive me.
The time to change the light bulb in my tortoise enclosure has finally come. Previously "he"(not sure yet) had an arcadia 12% uvb bulb. It's been in there since June with around 2 months not being used. I went to the place I always get my bulbs from but they only had 6% uvb ones. I got one and...