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advice needed concerning my labs and methylcobalamin and methylfolate

Hi, first of all I want to thank you all for sharing all you have on this site. It's been very inspiring to read your stories and your efforts. Have been trying to muster enough of my remaining brain cells to write a coherent post. I need advice. To make it short, I was clinically diagnosed with Lyme and possible co-infections almost three years ago. It has been impossible to shake off a terrible brain fog, which is as devastating as the chronic exhaustion and weakness. My wonderful, full, hard-won life as I knew it and loved it is essentially over....It has been like dying alive...I see that many of you here have been through this...

I went to see an infectious disease specialist this past April 2015 and he found few irregularities in my labs, and no Lyme. Instead I showed a high positive for Rocky Mountain Spotted Fever, which had gone untreated, and which I must have had years ago as a child in Texas. The lab also identified a unknown protozoa with very thick biofilms in my blood, which the doctor thinks is a cousin of malaria. (Which I apparently caught doing humanitarian work in Mexico among the very poor in October 2012.) But the doctor remarked that I was the healthiest of any of his patients with my illnesses and that my bloodwork looks normal in almost every respect except:
my platelets are high at 488
my cardiac proteins are high at 9.76
my b-12 is high, at 1447
my folic acid/folate is 19.9

Well, on my own, about two weeks ago, I decided to start Freddd's protocol, as so many of my symptoms mirror those of a b-12 deficiency...I started slow and felt amazingly better very quickly -- I want to say about 1/3 'cured' which is shocking because three years of treatments have not helped as much as these vitamins did in one week! I increased my dosages over the days as I had no unpleasant side effects except for a sort of dermatitis on my throat just behind my ears and a sort of darkening effect that comes and goes high over my upper abdomen....for the past few days I have stayed at
methylfolate 8 mg methylcobalamin 40-50 mg dibencozide 30-40 mg in divided doses
I also got some SAM-e, some P-5-P and some phosphatidyl serine, added that in, and I felt it helping...
I have been concerned about adding in LCF as I am hypothyroid and take 75 mcg daily...

meanwhile, I am not sure how to read my folic acid number, or what to think about my high b-12 blood serum...
and maybe I don't need the methylfolate at such high amounts?
i felt increasingly well on this protocol but now have started menstruating and am a little weaker (but returned to a 28 day cycle after having been on a 26 day cycle since I have been ill which feels like a marvel!) The skin on my arms and face which had withered in a strange way is drastically recovering and nearly all my fibromyalgia is gone...my memory feels somewhat sharper, too, already, and my mood has dramatically improved...my short term memory is improving...
is it possible though that I don't need the methylfolate and just have a b-12 deficiency caused by my chronic illness? how would I know?

I have stopped taking my multi-vitamin and my b complex, as I don't want to take anymore inactive vitamins. I am taking E and C and D separately, and have bioactive forms of the b vitamins on their way in the mail.
I am also wondering if I sound like a good candidate for the methylcobalamin shots, but they seem so expensive....and I am not sure about where to order for the best deal on high doses...

any advice concerning labs that might help me isolate my problem better? I need to return to my regular local doctor in a couple of months concerning my thyroid and could ask for them then...

thank you in advance for any responses...
victoria