Where To Take A Stray Kitten?

I have a two year old Morkie. He is a huge cuddler and loves to be with us all the time. However, he has grown very attached to our six month old German Shepherd puppy who just recently started sleeping in his crate at night. I always let them out together for potty breaks & playtime but now that she’s been sleeping in her crate, he doesn’t want to leave her side. This is creating separation anxiety issues as well as making me feel guilty that I am not allowing him more “alone” time with me (he had free run of house before).

Any advice? How do you handle this type of separation anxiety?? Has anyone here ever dealt with it?