The transfer case shifter would either interfere with the vertical side of the console or exit outside of it, depending on the T/C used and the linkage. The Ranger's transmission shifter and boot take up almost all of the space available in the opening of the Ex console.
Here is a pic of an 01 Explorer with a stock console and a manual T/C conversion. It has a V8, 4R70W and a BW4406, so it's a bit different from what you're thinking about. The shifter fits into a small box on the side of the tunnel (under the carpet). It is completely outside of the console.
The factory T/C shifter position on my Ranger 1354M is positioned more inboard on the trans tunnel. I believe that it would not work at all with a stock Ex console because the shifter comes up right where the side of the console would be. The way mine is laid out, it looks like you would need to make the console wider to include the T/C shifter and boot. I don't think it's a practical combination.