I am no clubfitter and hence am no expert at these things; the suggestion to take 1/2" off the tip is to stiffen the shaft a bit, probably more for spin reasons as opposed to launch or feel. So therefore, you would cut 1/2" off the tip, then assemble the head onto the shaft, and then cut to the 39.75" length from the butt end (which would be 39.50" allowing for the .25" when you install the grip, subject to my guess about EOD below.
Because of all that, if you wanted the shaft to be cut exactly to the length you would need, and that the tip end of the shaft is not all the way down to the level of the sole of the club (unless it is a bore through), you would need to know the distance between the bottom of the hosel neck and the sole of the club.
My advice on that is to cut 1/2" off the tip, and then cut the butt for length when assembling the club. That way, you will always get it right.
Re EOD, I have no idea what that means other than maybe End Of Dowel, which could mean length of club to end of shaft without grip. If I am right, then it looks like you were fitted for standard length.
I am sure that others will chime in as to what it means,