If you were low for a long time before you discovered it, it will take longer than you think to heal up completely. The body sends B12 all over to do many jobs... it is stored in the liver, and goes into the spinal fluid that bathes the brain. Sometimes during healing other priorities may occur and the nerves have to wait again for more B12. Most of the people with pernicious anemia, have good periods and minor relapses over weeks and months, as this process goes on in the body on its own schedule and terms.

You are not really that "high" yet with B12... high is over 1000.
You are better than you were, but this is all new and temporary...and healing is not quick. A good low homocysteine reflects that your folate and B6 are working with the B12.

I think you still have a long road ahead of you.
Do you use iron to treat your thalassemia? It would be a terrible twist of fate to inherit hemochromatosis along with your anemia.
Too much iron will deposit in the body and cause nerve symptoms. This would have to be evaluated by a doctor ..
hemochromatosis is not that rare as some doctors think.

Iron overload is one complication of treatment for thalassemia
according to this wiki explanation:
http://en.wikipedia.org/wiki/Beta-thalassemia