[UncleSalty]

Definitely don't take away his crate, it is currently the only place he feels safe. Start by feeding and watering him inside the crate, placing the dishes inside near the door.

After a day or too, start placing the food and water immediately outside the door of the crate.

After a few more days of that, move the dishes far enough that he has to stand halfway out of the crate to reach them.

Continue to move his food and water slightly farther every day until he is comfortable coming completely out of the crate.

Crate training is very healthy, despite the anthropomorphic feeling that humans view it as a cage. Dogs spend most of their lives sleeping and relaxing, and they prefer nice cozy enclosed spaces.

For the bathroom issue, he will hold it as long as he possibly can to avoid soiling the space he calls home. Just keep taking him outside every hour or two for 5-10 minutes at a time until he goes. If he doesn't go, take him directly back to the crate until another hour or two passes. Once he does his business outside, praise the hell out of him, big happy smile and friendly tone of voice, like he just won the grand prize for best dog in the world. Simultaneously give him something really yummy like a piece of processed cheese.

Good luck!