I would continue having him eat in the crate and play games that associate the crate with good things. Stuffed kongs are great for crate time. I would start by only shutting the door a few seconds and then open it back up again, praise him for not crying. Do this until you can leave the door shut for a while without him protesting. Eventually you want to be able to leave the room without him crying.
Now, for bedtime, he's crying because he's been left alone - he's just a baby so that's to be expected. I am pretty sure you are going to want your new pup to sleep in a secure area until he's trustworthy, too - is moving the crate into your bedroom not an option? I had to move Rowdy's by my bed until he got a little older - while he wasn't fully acclimated to the crate, some how sleeping next to me while secure in his crate didn't bother him at all. You might give it a try.
Now, for bedtime, he's crying because he's been left alone - he's just a baby so that's to be expected. I am pretty sure you are going to want your new pup to sleep in a secure area until he's trustworthy, too - is moving the crate into your bedroom not an option? I had to move Rowdy's by my bed until he got a little older - while he wasn't fully acclimated to the crate, some how sleeping next to me while secure in his crate didn't bother him at all. You might give it a try.