Does my employer have to accommodate what my Dr note says about no prolonged standing?

The first question that must be answered is whether your Lyme disease renders you "disabled" within the meaning of the ADA, and ADAAA. "Disabled" means that you are substantially limited in a major life function. The term is interpreted as broadly as possible to include as many people as possible.  To answer this question we would have to know how severe your Lyme disease is; what effects does it have upon your daily life activities. If you do qualify as being "disabled" the next question is what kind of accommodations do you need?  The employer, at the least is required to engage with you in an "interactive dialogue" (which means listening and speaking on both sides) to determine what accommodations are required, what the impact of making the accommodation would be on the employer economically, and practically in the workplace, and whether there are other less burdensome alterations in the working environment, equipment, or non-essential job functions. Ultimately once the employer has engaged in this process and has answers to these questions it is the employer's preference that will govern. The employer need not adopt the accommodation specified by your doctor, if there are other accommodations that would enable you to perform the essential job functions in a manner that is satisfactory to the employer. Thus while your employer must consider the doctor's recommendation, he is not necessarily required to follow it if there are other accommodations that will allow you to do the job. You work for the employer, not the doctor.