I see 3 things so far, but I have not studied the charts on your link fully yet.

1) you might need some carnitine support.

2) the acidosis is created by two acid problems. The most obvious one is lactic acidosis. This affects muscles. This may be why your leg spasms after activity.

3) you will most likely need biotin supplements for life.

One article I read today says people with only one good copy of the normal gene may only show symptoms when stressed as adults. This means you need to watch physical fatigue carefully.

To start with, I have a suggestion for the acidosis. I am using this now myself... Alka Seltzer Gold. This is the alkaseltzer without aspirin. It is only available online and not in stores. If you read the reviews, you find Lyme patients use the Gold to reduce Lyme pain. I found that very intriguing, since most Lyme pain is nerve pain.

Amazon.com: Alka-Seltzer Gold Tablets- Non-Aspirin, 36 Count Box: Health & Personal Care

This formula is similar to a product doctor's use called
K-salts. K-salts are used to block sudden allergic reactions in children by specialists in allergies and environmental doctors.

It is more complete, the Gold, than plain bicarbonate tablets.
I'd try them if I were you. Start by using one tablet which 1/2 of the dual pack they come as. I am using only one tablet a day now, and it appears to be working. Helping allergies and my severe knee attack which might have been gout. I have borderline high uric acid for many years, but the doctor says no treatment is really necessary for it. duh? But my knee which was extremely acute, is now no longer like that. I have pain level 2 in it now compared to the pain 10 when the sudden attack happened.
When I searched OTC gout treatments, bicarbonate came up at many sites.

I noticed other improvements too with the Gold-- my stinging eyes stopped, my toes stopped hurting at night, and I am sleeping better.

So I think it is worthwhile to try AlkaSeltzer Gold and see what happens for you. Post to me after you have been doing one tablet each day, and we'll see how you react. You might need more, but my response to just one, tells me that it might be a very subtle thing and a low dose may be all you need.

And I'd stop the benfotiamine for now and try low dose carnitine instead. 250mg, or if you cannot find it, then 500mg a day for a month. See how you feel.

I also saw on one of your charts, that lysine is blocked with this deficiency. Since lysine is so inexpensive and benign to take you might need this too. But it is your decision to take it. I am not sure how lysine fits in with this deficiency.

It is amazing how little we understand about our biochemistries.
You would have never known this without that test, and no doctor would have diagnosed you with this genetic mutation either. If you are married and plan to have children I'd have your husband take the DNA test too. If he is running on 1/2 biotin levels...you could have a child who could be really in trouble.