A computer-assisted medical device is configured and used to endoluminally navigate to a location in the gastrointestinal system and there treat certain body lumen wall areas while avoiding other body lumen wall areas. Embodiments ablate the inner mucosal layer and sub-mucosal nerve plexus of the stomach, duodenum and jejunum to effect treatment of insulin resistance and metabolic disorders, such as Type II diabetes (T2D), polycystic ovarian syndrome (PCOS), non-alcoholic steatohepatitis (NASH), non-alcoholic fatty liver disease (NAFLD), congestive heart failure (CHF) and obstructive sleep apnea (OSA). Various sensors are used to assist a clinical operator to navigate from the mouth through the pyloric sphincter and into and through the duodenum and/or jejunum. Various sensors are used to map and identify portions of the duodenum and/or jejunum. Various lumen wall ablation devices and methods are described. Various post-treatment assessments are described.