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Toby has had a fungal infection now for at least 2 months. I didn't notice it at all until the day I moved him to a friend's house to care for him while I was out if the country for 2 weeks. It's my first time experiencing something like this, so I didn't know how serious it was and when I came back I found that it had gotten pretty bad.

Now I'm using a treatment found on Japanese websites (I live in Japan). It's a home remedy of bathing him in Isojin... A kind of Japanese gargling medicine. The internet says it can also be called Isodine. Japanese language forums swear by it for curing fungus. I apply it heavily with a towel and then dry dock him. He hates being dry docked, and aside from the coloration (that has completely stopped growing now...but isn't going away), he seems perfectly healthy. He's very active, eats a lot and always wants more, and overall seems happy/healthy.
...but the white coloration isn't going away...
Should I be doing more?
Is this slowly killing him while I'm thinking he's happy/healthy?

I'm trying to upload photos from my iPhone, but it says the filesize is to big. I'll try to figure out how to shrink iPhone photos.

Apparently there's an app for that. ^^
Here's the photos.

By the way...I'm also aware he's pyramiding. >.<
I've completely changed his diet over the past month or so to mostly veggies instead of the only-pellet diet he was on. Didn't think I was giving him too much, but seems like I was.

Don't beat yourself up over this. Shell fungus is very aggressive and not always a result of poor care.

Was the Japanese treatment specifically for turtles? There are likely various strains of fungi, so treatment might not always be effective.

From what I've seen… fungus alone is not going to hurt your turtle. However, it can cause retained scutes and allow for secondary infections that can be dangerous.