Where the girl is digging in the dirt and finds the key that has #1 on it and the little kid shows up and says 'Whores don't get a second chance' and the fat guy says it as he grabs his doctor and they swerve off the road

that in theaters the quick cuts of the killer identity killing everyone was just the little boy. In the extended cut there are some shots where the killer is actually the boy and the fat bald guy. I assume it was to show that the boy was really Malcolm's true identity, but it was probably cut due to it being confusing to some.

In the Theatrical Cut, you see the young boy and he commits/is somehow involved in each of the other murders.

In the Extended Cut, the director inserts quick flashes of the bald-headed killer actually committing the crimes as well (he's wearing a blue flannel shirt - the flashes each last about 1 second or 2). There's a great scene of him holding a bloody knfe after stabbing one of the victims on a bed.

NOTE: To help you out, be sure to watch the Theatrical Cut with the Director's Comments "ON" - you can't hear director's comments regarding the Extended other version and why he took those few seconds out. He mentions that the other, extended ending (with the actual bald-headed killer appearing in quick flashes) was either too confusing or too obvious or something like that. He says that by inserting the bald-headed killer into the final scenes, the audience's interpretation of the movie might have been changed, and he wanted the biggest "Oh, neat!" shock to be that the characters were various fragments of the killer's imagination, and NOT that the boy was the remaining killer fragment of his mind.

There is an extra scene in the judge's chambers when the doctor (Alfred Molina) arrives.

The extended finale is just cuts of Malcolm Rivers (Pruit Taylor Vince) committing the real world murders he was charged for, which is added to the cuts of the little boy murdering the other identities.