Great Dane, strange behavior

Question
I have a 5 year old Great Dane (Abe), who has been with us since he was 7
weeks old.  He is an indoor dog/member of the family and has always been
great.  About a month ago he started waking up around 2 or 3 am and
standing next to the bed whining and shaking.  We have tried several different
things to get him to stop, but our patience in running out.  He has been
keeping us up from 2 or 3 am until we have to go to work.  Here are a list of
ideas we had that could be bothering him.
1) We have tried letting him out repeatedly at night, thinking maybe he needs
to use the bathroom.  He just stands on the back porch.
2) We thought it was bothering him that we put our 7 month old son in his
own room downstairs (he had been sleeping in our room), so we put another
dog bed in his room, so that Abe could sleep there as well.  This did not help
at all.
3) We thought that he was was hungry, so we gave him extra food.  He slept
for a couple of nights and then it was back to the whining and shaking.

I've had the stomach flu this week and was home during the day alone with
Abe and in the middle of the afternoon, he started shaking, tucked his tail,
and stood next to the bed whining like he has been doing at night.  Last night
we didn't sleep much at all.  When Abe is like this, it's almost like his mind is
in another place, he won't listen to us and acts terrified.  We love him so
much and want our happy big dog back.  Any ideas?

Answer
Any unusual behavior requires veterinary attention.  Although this may be behavioral (and certainly all you've attempted to help him may have actually rewarded the behavior and worsened it), it MAY BE physiological.  The dog may be in pain or be having low level temporal lobe seizures.  He needs FULL evaluation, super blood chemistry, and I'd do a full body x-ray.  The vet should do a urine extraction and you need to bring a stool sample.  Do this ASAP.  I don't want to alarm you, but this behavior sounds similar to that of a dog I had many years ago whose life I was unable to save.  IF it turns out not to be physiological (after all those tests, absolutely demand they be done), I will be greatly relieved, as will you, and you can repost for behavior modification to extinguish this problem behavior.  Please remind me of the original problem when you repost (as I read so many of these questions every day, I can't always remember what's what.)