Reddit mentions of Comfort Zone with Adaptil Diffuser for Dogs (Discontinued by Manufacturer)

Separation anxiety is a big problem in a lot of dogs, and needs to be addressed quickly. That being said, don't expect your dog to change overnight. Here's some of the techniques that worked wonders for my dog.

The most important thing to address is how you leave your house, and how you come back. One time when you're headed out, write down everything you do before you leave: pick up your keys, put on your shoes, open your door, whatever. Chances are you have some kind of ritual, and your dog has made the connection between these actions and you leaving. Break the connection by doing all the actions on your list repeatedly without leaving. I spent hours fiddling with my door locks, putting my shoes on and off, and grabbing various items around my house, until my dog learned that these things do not necessarily mean that I'm leaving.

Equally important: you don't want him to think of your return to the house as a special time. You will need to leave your house for short periods of time (say about 10 seconds), and when you go back in, your response should depend on what he does. If by the time you walk back in, he made it to the door and/or started crying, ignore him. Look up and away. If he tries to force himself into your field of view, turn around. Don't give him the slightest bit of attention. Eventually, he will give up, lie down, or do some other relaxed behavior. The moment he does that, praise him! Feel free to offer a treat, and once he understands he did something right, leave the house again. You will keep this up until he stops coming to the door and/or crying. When you can leave the house for a few seconds without him getting anxious, you no longer have to ignore him. Don't praise him too much either, just acknowledge his existence and get on with your day. Then, you should start leaving him alone for longer periods of time (again, ignoring him if he's anxious, slight praise if he's not). From my personal experience, once you can stand outside for about 5 minutes without your dog reacting, you're good to go.

It may take a long time before his behavior improves significantly, but there are some ways to make it easier. Exercise is very important. If your tire your dog out before you leave, he literally won't have the energy to destroy your house. Try teaching him to fetch, and throw a ball at him for half an hour in the morning. Keep in mind that this works hand in hand with training, as a dogs energy returns quickly. That being said, a tired dog is much easier to train then a hyper one.

Finally, there are products that aid (again, hand in hand with training) anxious dogs. My favorite is called D.A.P. (dog appeasement pheromone). It's a pheromone that comes from a nursing dog, and has been proven to calm dogs with anxiety. It's available as an diffuser, and a scented collar. I recommend using both concurrently.
That's all I can think of now. I'm currently at work and writing this on an iPhone, so I'll edit it/ add anything I can think of once I get home in a few hours.

EDIT: for clarity. Also, so i can link some examples of DAP Products

Diffuser

Collar

As far as the noise issue... my dog is also afraid of noises. I didn't realize this was part of her separation anxiety. She's torn up doors/door knobs,etc. I hired a dog walker (not what I'm suggesting for you) and she noticed that it seems to be noises that scare my dog. It makes me feel like an idiot for not noticing. I tripped over my flip flop on a walk last week - it scared my dog and her teeth chattered and she wouldn't come near me for a bit. So I purchased this: http://www.amazon.com/gp/product/B006SFUEF2/ref=oh_details_o00_s00_i00?ie=UTF8&psc=1 white noise machine. I ordered this particular type only because it was relatively inexpensive. I actually got two - one for upstairs and one for down, but I can turn the volume way up on the one downstairs and it can be heard upstairs as well. I only got it yesterday but so far it is like I've drugged her. She slept all night long, and as I type, she's asleep on my couch instead of pacing around like a nervous nelly. She hasn't even barked at my neighbors when they walked outside with their dog. That in and of itself is amazing.

Your dog does seem to have confidence issues. I don't know what to do about the rest. You do not seem like a bad person. I have worked and worked with my dog to give her a home she feels safe in, and when she doesn't, it hurts. We can't fix everything.

Also, my dog walker says that she has had success with DAP: http://www.amazon.com/Comfort-Zone-Diffuser-Single-Refill/dp/B003E71E06/ref=sr_1_cc_2?s=aps&ie=UTF8&qid=1371901678&sr=1-2-catcorr&keywords=DAP
Which is supposed to calm dogs. I'm skeptical, even though my dog trainer from two years ago that trains police dogs and fixes 'ruined' dogs also suggested. It's a pheromone. I haven't tried it, but I think I will. THese solutions all take money.

My dog barks and barks at people when she wants attention. I did not realize this for the longest time. (I feel kind of dumb admitting this.) I brought a new guy i was seeing over to the house. She barked at him, and he said "Is she going to bite me?" and only 1/2 joking I said "I don't know". He stayed with me for 3 days (he lives in another state) and the next day I had to work. She barked at him until he sat on the ground and then they became friends. Likewise, my sister and her family came over and my dog barked at my brother-in-law and he looked at her and said "What ARE you barking at???" and she huffed and turned around and ran up to my nephew and barked at him so he said the same thing and then she ran to my side and lied down. I don't know that any of this is helpful. But it is all a process.

I have a friend with a dog with pretty severe separation anxiety. She said this worked for her. Seems like it's about 50/50 for dogs, but for $20, it might be worth seeing if it works for you.

http://www.amazon.com/Comfort-Zone-Diffuser-Single-Refill/dp/B003E71E06/ref=sr_1_1?ie=UTF8&qid=1409810479&sr=8-1&keywords=DAP+infuser

When you let him out of the room when you get home, do you do it quietly? Like just leash him up, take him out- no talking to him, no excited voice, etc? Lots of folks forget that we ramp our dogs up a lot of the time when they might stay calmer (I mean, he's a puppy and he's happy to see you- it's not like he's going to be chill) if you are calm and quiet. A friend with a dog that pee-d in excitement used to ignore his dog for the first half hour he was home. Tough to do, but it worked- that was also an older dog, so tough to do with a puppy. When I get home, I talk nice to mine (adult dogs) but quietly and they don't jump or get too nuts. They are super wiggly and such, but not jumping and barking like I see some people's dogs doing. Just a thought. Might help enough to stop you having to clean up pee as often. You'll have to get your Dad to greet him the way you do- consistency with puppies is incredibly important. Nice of him to help you out, though! Four hours or less is really awesome.