1a) Er thought: She has paid everything. (He thought that she had paid everything)
1b) He was afraid: She has paid everything. (He was afraid that she had paid everything.)
2a) He knew: She had an accident.
(He knew that she had had an accident.)
2b) He was afraid: She had an accident. (He was afraid that she had had an accident.)
3a) He thought: She will pass the exam. (He thought that she would pass the exam.)
3b) He hoped: She will pass the exam. (He hoped that she would pass the exam.)
4a) He assumed: She goes to school. (He assumed that she went to school.)
4b) He wanted: She goes to school.
(He wanted that she went to school.)