I think it depends on what exhaust you bought and if you want to get the most out of it. If you have a full flow exhaust, go ahead and pull the snorkel. Then perform the L mod but buy some plugs the same size if you think you didn't need to. I say there is a noticeable difference. .. Air in, air out. Its not rocket science. The Lmod holes are under the seat and as high or higher than the snorkel, Were you planning on swimming with your KLR? ;-)
"Where ever you are, there you go..."