Can you adjust the height on a sunroof so it sits flush with the roof? 2006 taurus

Yes, the factory installed sliding roof can have the "timing" set and adjustments can be made. I suggest you locate the Ford service manual '06 Tauras Or (search online) check the body section it has an in depth explanation of the roof operations. Regards

Working on sliding, electric sun/moon roofs is a Zen exercise- they are complicated- if you can not see how that thing works, better get a good mechanic to do it-