Don't have a problem with the E prefix to the serial number. Some look like that.
What I find interesting is that some of the markings, particularly on the barrel, look like they have been buffed. They are not very sharp. There should be burnishing around the ordnance bomb and Winchester proof mark on the barrel. I'm not seeing that in your photos. Also, there appears to be a punch mark on the barrel next to the Winchester proof mark. Is there also a punch mark on the top of the receiver? These punch marks are thought to be rebuild marks. And there are even some collectors who believe that Winchester actually refinished some of these guns either near the end of or just after WW2, and that Winchester applied these punch marks on those refinished guns.
You said there is no evidence of a filed down sight bead on the barrel, right? Because some of the late made M97 trench guns have barrels with the filed down bead sight.
Post more photos, if you can.