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Last time I inquired with a builder of trans, I was told : 400 is larger and has more HP loss, but can be built stronger than a 350. I did not go with the automatic so I have no real life experience..
With todays new developments I would think they can be about equally as strong.
The 400 is way stronger than the 350-- even built using good parts. But it's also a bunch heavier. That said, some years ago I built a TH350 for a guy that was running a 455 in a 66 GTO with slicks and 4.11 gears. He broke everything but the trans.
When I worked at Chevy they sent a few of us to the new TH350 trans school. Then the TH400 came out behind the BB cars and in trucks. When asked if we had to go to TH400 school, the service manager said " no use, they dont break down, to strong".