Thanks for your posts everybody.
Muddy and I arrived 9 minutes late for his exam and then got bumped and had to wait about 40 minutes. It's a busy place though so you really need to get there on time to keep your slot. Darned ferry!!!
The vet was great and spent alot of time with us when she finally came in. I showed her the video of Muddy hacking and thankfully, he did it for her in the room. They did xrays and in-house blood work. She said that if a push pin was lodged, the metal would show up clearly on the xrays. I was also worried about heart problems but the xrays showed that he has tracheal membrane inflammation. She was surprised because she said this is the kind of thing you see in Yorkies and Pugs. She said that with smaller dogs their tracheas would most likely have collapsed but because Muddy is a big dog his throat is staying open.

She didn't know what caused it but she said that his attempts to cough are irritating his trachea membrane and the inflammed membrane is making him cough! She said the key is to get him to stop coughing and prescribed Benylin DM 50-60mg every 8 hours. She thinks it will clear up.

His blood work was pretty good and his white blood cell count was normal so he doesn't seem to be fighting an infection. His BUN and creatinin (spelling??) levels were up and she called it Azotemia. She said that it was an indicator that he is beginning to have issues with his kidneys so I have to switch him over to K/D or some other low protein food.

Here is the worst news though. One of our dogs has been pooping on the floor and we weren't sure who it was but have suspected Muddy. While at the vet I told her about that and said that the boys are very good about waiting until morning but someone has been going on the floor a half dozen times in the last 3 weeks. It is worse when we feed wet food so they are just on dry now. I also told her that Muddy sometimes drags his back right leg sometimes. He is very active and runs around like a crazyman still and continues to try to dominate Finn by mounting him. But he does drag that foot every now and then, just for a second, kind of like a lazy step. She took xrays of his legs and hips and said that he seems to have a bit of arthritis on his left side but that doesn't explain the lazy foot on the right side. She thinks he has Degenerative Myelopathy (a degeneration of his spinal area) which is not uncommon for his breed and causes things like foot dragging and incontinence with regard to defecation. She said it's one of those diseases that you diagnose by ruling other things out. I asked her if it was still possible that the inappropriate pooping might be dietary related or maybe it's Finn and the foot dragging might be arthritis? She said it could be but she felt it was Degenerative Myelopathy. She said there is no treatment for it and it can progress quickly, anywhere from a few months to a dog she knows of that was diagnosed a year and a half ago and is still able to walk.
She did give me a few websites to check out and said there is a place in Florida that is trying a treatment plan that is full of all kind of things like supplements and holistic treatment but it is very new.

We are feeling very down but at the same time, we are so relieved that he doesn't have congestive heart failure which would have given us even less time with him. I'm going to Google the degenerative disease and see what I can learn so we can help him the best we can. He's such a great dog.
Is anyone here on PT familiar with this disease? Any info would be greatly appreciated.