Re: My 1917 Eddystone
No, I'm not sure what the 'W' or 'M' stands for, but it doesn't stand for Winchester. The barrels were stamped with the makers initial right being the front site (W-Winchester, E-Eddystone, R-Remington). I have never seen 'JA' before, and I did a search on Google and found that 'JA' stands for "Johnson Automatic". According to what I read, they are replacement barrels that a few of these rifles got during WWII.
My guess is that your barrel has two grooves, instead of the usual five. Nothing wrong with that though.
As far as cutting the site hood off...maybe whoever had it before planned on mounting a scope to it, and thought the scope wouldn't see over the "ears".