I do standalones a lot. Using a an auto tune is not an issue at all. But I do recommend having a speed sensor input of some sort. I can post up the ones I use if you need them, fit any transmission with a speedo cable output. If you dont use them some idle and timing tables are not referanced. With a speed sensor stand alone harness on auto tune you end up increasing running airflow more than normal to keep it from stalling, but beyond that it runs great.