Print Alignment Anomaly Troubleshooting Request

If youre printing on actual 6" x 8" paper, you should set a Custom page size in your Print dialog. Also, make sure your orientationj is correct. in your screen shots, you're 90° off.

As for making a PDF, that should never be done from the Print Dialog in ID. Export it from the File > Adobe PDF Presets menu. For your purpose, try either Press Quality or High Quality. No need to change any of the options when you Export.

But since you have a special paper size, you will need to configure Acrobat accordingly. (Page setup > Paper size > Manage Custom Sizes....)