I am trying to take a picture of a long counter in a super market. It is about 15 yards long. I inched along (at about a distance of 3 yards) and took straight on 30-35 pictures with my 16-35mm at around 16mm. I also did another series (with more images) at 35mm. 

When I was at the computer and wanted to stitch them together I noticed that it just would not work, even though I had enough overlap. But the angles had changed. The items behind the glass of the counter would have slighly different "sides" showing forward which made it impossible to stich. Even worse was the "background" - only being 1 or 2 yards behind the counters items moved closer and farther away from objects on the counters (i.e. scales). 

I then made a test taking more pictures - but the problem with the background remained. What is the right approach to taking such pictures? What focal length is the best for this?

Thanks