Is the 400 in a 1968 Bonneville a small block 400?

No there is no "big" or "small" block Pontiacs. The terms "small" and "big" block are Chevy & Ford terms. Pontiac blocks were thesame physical size from the 1955 287 right through the last 400 cast in 1978. All blocks had a bore centerline of 4.62 inches, which puts them right between the small block Chevy (4.40 inches) and the big block Chevy (4.84 inches). There were short deck versions built- the 1969-1970 303 race engine (about 25 made), and the production 265,301 built from 1977-1981.

ALL 287,316,326,350,347,370,389,400,421,428,455 engines are the same exterior block dimensions.