You may find a plastic strip curtain especially for a dog kennel useful. I got a couple from Zooplus:
http://www.zooplus.co.uk/shop/dogs/dog_kennels_flaps/dog_houses/woody/95890My shelter has cat-flaps however my feral doesn't seem to know how to use them yet so I have propped one of the flaps open and placed the plastic curtain sort of over the top of the open cat flap - taping it to the top of the box. This way he can get inside and the plastic curtain blocks the wind to some extent. I have lined my shelter with Thermawrap which is a great, easy to cut to size, product from Homebase. I taped it to the inside of the shelter including floor, roof and sides. I have placed a small Flectabed inside (upon advice of Mark on here) and the inside is filled with straw. I was going to use hay but the pet shop advised me to get straw as it has better thermal qualities and doesn't absorb water as much as hay. Propably not a problem so much with an enclosed shelter. I have recently bought a Snugglesafe heat pad although I now need to put a bigger cat-flap in the shelter so I can get it inside!
To stop the rain from getting in the door it can also help to make a little awning to place over the top of the opening. You can make this from a two to three inch wide strip of cardboard covered in bin liners and taped above the door.
I've been trying to post a picture to let you see what I mean about the awning but I think the file size is too big.
Could you make the opening smaller by putting a strip of cardboard covered in bin liners across the bottom of the door opening?
I have got a blog where I have posted detailed instructions with pictures on how how to make an emergency shelter so if anyone wants the link please PM me. Don't know if I'm allowed to post it here.
I was also wondering about a sheltered feeding area. I do have a porch however I was thinking of making an extension to the shelter or an overturn cardboard box covered in bin liners with one side cut out and maybe some polystrene as a flooring.
Hope you find some good solutions I know what it's like trying to keep them warm and cosy.