If you're a powder coater by trade, IDK why you wouldn't. Yeah, you might strip bolts, and yeah, it might be a pain. But I feel it's all worth it.
I had the turbine and center section that I was going to use on my bus cerakoted by a buddy. He quit doing it before I could have him do the manifold, and the project is still sitting there unfinished. Oddly enough my turbo was off an 02 dt466e, but I'm not sure if it's the same as yours. You can read about the steps I took in my build thread, as I de-rusted it in a molasses-water solution and it came out awesome.
As I said, I haven't used the turbo, and I've actually listed it for sale on marketplace. New chra, cerakoted cartridge and exhaust housing, essentially a new piece. I'd sell and ship on here if you need it.
As far as the pyrometer is concerned, in the bend right before the Y, in either front or back pipe. Back of the engine typically runs hotter, so I'd choose back.
This guy here has a dt360, but it should be similar to your 466, and he puts it in the exhaust flow in the right spot.
I just watched cassady's video, and my god did he do that wrong. Like you, he has a divided manifold and turbine housing, and there is no way that thermocouple is in the exhaust gases with where he put it. It's kind of disappointing because a lot of folks rave about him and his knowledge/skills.