Labs are very owner-oriented dogs and will hate being away from you, especially at night when it's dark and lonely and everyone you love has disappeared upstairs! Our have both slept in our bedroom from day one and as a result learnt to settle very quickly. I realise that's not always practical, especially if you've got three flights of stairs to negotiate at toilet time, but he obviously settled better being upstairs with you, so I'd probably continue with this for an easy life (and some sleep!). Once he knows he's not going to be left alone at night, you might find he's more accepting of being left for short periods during the day. Kongs do only tend to have a limited attention span (freezing the contents can make it last a bit longer, and will also help his teething), so if you can give him a couple of choices it's better. But ideallu you want him to sleep when you leave. Have you tried leaving a light and a radio on in the kicthen when you leave, so he doesn't feel so alone?
With regards to the howling, what do you do when he's doing this? Do you return to the room, speak to him, shush him, scold him? Dogs crave attention and even negative attention is better than nothing, so it's best to just ignore him. If he howls when you leave, don't give in and go back to him, just give a stern 'no' from wherever you are. And when you go back into the room, don't make eye contact, and don't acknowledge him straight away. Even better, if you can open the door and walk into the garden, wait for him to follow you outside and then acknowledge he's there.
With the peeing and pooing in the house - do you always make him go in exactly the same spot in the garden? If not, he may be associating his rewards with the act of going to the toilet, rather than the place. He might thinks you're so happy when he does a poo, he'll do one right in the kitchen for you too! And then he'll be confused about being shouted at when he's been such a good boy going to the toilet. Also, if he's always going in the same place, make sure to clean it with biological washing powder or a special pet odour spray, otherwise the smell will keep drawing him back.
Just an afterthought really, but do you think he's learnt to see his crate as a bad place? It's supposed to be his den, so if he's only getting put into it when he's going to be left alone, the crate training won't work. As much of a hassle as it is, bringing his crate into the main living area (open, to use as his bed) whenever you're in there may help him to accept it, as he'll know he doesn't just get put in there when it's alone time.