We will take amtrak from sfo, is this lodge close to the train station? How do we get to the lodge from train station?

The lodge is about 80 miles from the Amtrak station in Merced if that's where you're going. You'll have to transfer to a YARTS bus to get to the valley. I'm pretty sure that the YARTS bus stops at the lodge. I've never tried taking an Amtrak to Yosemite, so I may be wrong.

Not sure how close Amtrak is to Yosimite Valley .. The buses in the Valley run to different points in the Valley...try to Google Amtrak from your location to Yosimite..

Yes, tbe bus stop at the lodge, very convenient.