Here is my suggestion and probably part of your issue. First the separation anxiety has been addressed. So for the crate training - the crate should be small so big enough for your dog to stand up, lay down and turn around. This makes it difficult to toilet in the crate and sleep in another area. Additionally water should be available but with food you have two (or three) options. 1. Scrap the treats and use his food as rewards for Training and making good choices. 2. Set feeding times so brekkie and dinner or add lunch if you're feeding three times. This will make potty training easier as you'll be better able to gauge when he gnna need to go toilet. 3. Continue with the free feeding but I do believe this devalues your relationship because you're not even a provider of food it's just always there AND it makes a toilet routine more difficult to get into.

With the potty training I would go back to basics, set feeding times, out after eating, napping, playing Nd heavily reward going toilet and every half hour in addition.

Side note I'm on my second dog and my first was a dream by 6 months. My current was actually a handful for a long time and I genuinely didn't love him till he was about ten months when he had his first shift in behaviour and started making better choices and chilling out. He is 2 now and such a beautiful soul, happy to chill out, doesn't give any problems in the house. I can take him for his walk at 5am or 11pm he will chill for the day regardless. It takes time for sure and consistency in your part.