You can configure timeout values in the Alfresco Transformation client by adding the relevant properties to the transformation engine configuration file in C:\\Program Files (x86)\\TransformationServer\\tomcat\\webapps\\transformation-server\\WEB-INF\\classes\\default-configuration.properties.
Use the code sample to set these timeouts:
# transformer timeout in seconds
transformer.timeout.default=300
transformer.timeout.word = ${transformer.timeout.default}
transformer.timeout.excel = ${transformer.timeout.default}
transformer.timeout.powerpoint = ${transformer.timeout.default}