Welcome to you and to Waffles! Is this your first basenji?
There's been some great advice already given… and as a mom, I'd like to gently remind you to try to "relax", lol. When Waffles gets anxious, try to do your best to remain calm and not to feed off of her frantic energy. I know some people are completely against sleeping with their dogs, but I must admit that all of our dogs sleep with humans, and they love to be under the covers.... normally by your feet.
By nature, basenjis love to be in packs, and perhaps Waffles is missing her family.
As for crate training, when my sister adopted her basenji, he had the same type of reaction as Waffles. When she would return home, she would immediately give her dog a treat while he was still in the kennel, then she would leave to put her purse away and come back in short order. At first, he would frantically paw at the gate until she came back, but since she made this a routine, he knew that yes, Mom left a treat, but she was coming back soon. When she opened the crate, she'd take him outside right away, with high praises for going to the bathroom, and a couple of treats for going potty. When they would get back inside, she would casually leave a couple of treats in the crate and leave the door open for him to find at his leisure.
In the morning, her routine is very similar: he sleeps in the bed, so before they go out for their morning walk, she will strategically position 2 - 3 treats on the counter (near the crate). He sees that the treats are there, but he doesn't get them until he goes outside, does his business, and return to his crate. He knows that he gets treats when he goes into and out of his crate, so he really is okay with this!
And a gentle reminder: adjust the food level to make sure Waffles isn't getting too many treats throughout the day. My dogs love their dog kibble enough that I can fortunately give regular food as treats.
Hugs and Roos! (Does Waffles roo?) We would love to see pictures when you get a chance.