What is going on with my body??

Hi-I just found this site and it's one of the best ones I've seen.  Thank you for providing a forum for what apparently is a very large community of people without answers.    I was diagnosed B12 deficient a year ago (July 2009) after experiencing a lot of neurological and physical symptoms.  I have been taking monthly B12 shots.  My level has not stabilized and is as low as it was a year ago-246.  This week, because I told Dr. I am still exhausted, they tested my Vitamin D level.  It registered at 12.5.  They told me the acceptable range is 30-80.  I'm now taking 5,000u 2x weekly for 8 weeks and then 1,000u daily thereafter.  
I don't know if you were tested, but I also have a positive ANA 1:640 H Speckled.  They said I was not positive for Lupus but none of the 'specialists' I had to see to 'rule-out' 800million things had any answer for 'why' my body is no longer absorbing B12 or why I'm ANA positive or why my D is so low.  Even my GP hasn't demonstrated any urgency in finding out what is causing my body to behave this way.
I'm a healthy 46/female and up until a year ago, I worked out with my trainer 3-5x a week and have always been very fit and healthy.  I can't even get to the gym-I'm exhausted all the time.  It's a palatable relief when I have a moment when I realize-"hey, I feel pretty good right now".
I'm sorry that this is way too much info, but I was wondering if you have any insight.   I'm all over the web and haven't found anything conclusive-only scary.
Thanks for your time and if you have any thoughts, I'd appreciate hearing them.

[rumpled]

I have low D and I just take 2-3000iu a day every day - it is ok when you are that low. You are probably not going to rise that fast (I still hover on low) and there is no reason to drop doses.
Are you seeing a GP, rheumy or endo? If just a GP, I would also venture out and see the other two as well - the rheumy may be able to get more testing and more out of the ANA test and there are hormonal issues that cause inflammation and low D and B. Those are ideas anyway.

[karajo]

There are several things that can cause an elevated ANA.  The speckled pattern is seen in SLE, numerous other autoimmune diseases and in some healthy individuals who show "low" amounts of antibody.  Your 640 is not "low".  

There are 11 criteria for a lupus dx.  You must have at least 4 of the 11 to recieve a dx.

They are:
1. malar rash over cheeks (butterfly rash)
2. discoid rash, red raised patches
3. photosensitivity - reaction to sunlight, resulting in skin rash
4. oral and nose ulcers
5. arthritis
6. serositis - inflamation (inflammation) of the lining of the lung or heart
7. reanl disorder - excessive protein in urine and/or cellular casts
8. neurologic disorder - seizures, or psychosis
9. anemia or low white blood count or lymphopenia or low platelet count
10. positive ANA
11. positive anti-DNA or anti-Sm, or antiphospholipid antibody or false pos. syphilis test

Other symptoms are:
fever
abdominal pain
chest pain
shortness of breath
blood in urine
hair falling out
fatigue
muscle pain and weakness
dizziness
poor memory
headaches
poor circulation in fingers and toes
tingling in extremities
diarrhea
bloating
nausea
weight loss
abdominal pain
blurred vision
depression
palpitations
raynauds (where fingers turn white when cold)
intollerance to cold
sore throat
...to name a few

Keep in mind that fibromyalgia, CFS, MS and lymes disease also have similar symptoms.  

How many of the 11 criteria do you have?