39 year women w/o child would like children Still has ovulation but has diaphragmatic endometriosis. Need to make decision. Remove it or get pregnant?

Why either/or ? You might consider doing both, in whatever sequence you desire. Removing the troublesome area or areas may delay pregnancy, but by 40, women's risk of adverse outcome through age alone is just 1% above that of younger women. You may want to meet with a genetic counselor to identify any family,health and age specific risks and decide based on full knowledge of the possibilities.