So it can be surmised from this that the reason these mesopelagic fish have high contents of plastic is due to the fact the migrate closer to the surface to feed on fish presumably which are consuming smaller fish which are more intensely feeding in or around the plastic waste.

Yes, I would say so.

Can you tell me whether or not there was any deep water analysis done to calculate if any contamination from the plastic reaching down that far or is the plastic contamination localised to the upper levels of the ocean?

I'm pretty sure this research was based on the mesopelagic fish eating fish that would live closer to the surface. While plastic can sometimes end up "free floating" in the water column, it tends to either stay close to the surface or sink to the bottom. It all depends on the density of the water and the plastic.