Well, I would say what you are doing should help in the long term, you are attacking inflammation in a healthy way, by strengthening the bodies ability to do it by itself by eliminating the source, as well as promoting cell mediated immunity and thus the regulating abilities of the immune system. Your protocol is helping to ensure your homocysteine levels are low. You are also working to increase glutathione which will detox things that can aggravate the condition. Keep looking for and treating any conditions and problems/infections you can until you are healthy. As far as the other clotting factor, im not very well versed in that area. That would be a good area to research.
Orthostatic Intolerance. Caused by a loss of blood pressure/flow when standing. Very common with cfs. Sometimes other conditions that cause this are even mistaken for cfs. There are many theories and possible causes as to why this occurs, I believe in the case of cfs it is caused by lack of bloodflow/oxygen, due to cytokine induced capillary hypoperfusion (or in yours or other cases possibly thickening of the blood, or both) to certain areas of the brain which causes dysautonomia. There are other symptoms that can come with dysautonomia. It would also make sense that overall low blood flow caused by thick blood/hypercoagulation could cause some symptoms of OI by itself without dysautonomia being present. Look up the symptoms of them and see what you think. Low bood pressure can also occur with adrenal fatigue. Are you beginning to understand just how grey, murky, and overlapping all these conditions are?
You might need to cut back the adb12 when you start hydroxyb12. B12 and methylfolate need to be kept in balance. Unbeknownst to most, you can incur problems when using too much b12 too, though it is far less likely when not using mb12. When mb12 loses its methyl group it becomes highly reactive and can cause problems if not methylated again (by methylfolate) quickly. It can deplete other things if this doesnt happen. When using hydroxyb12, it is less of an issue because methylfolate pretty much becomes the limiting factor.