No, you do NOT need to remove the motor to replace the shaft. The manual says to do so, and the Kawi mechs will tell you that, too, but that is not the case.
I replaced my waterpump/balancer shaft after getting advice from experienced wrenchers, and it went well. You have to open both sides of the motor (easy), and the shaft comes out pretty easily.
I did replace the mechanical and oil seals while I was there, so it's best to have those parts on hand before you start. There is a small o-ring on the coolant impeller shaft that can get mangled up if you aren't careful (thread it on, don't push it on), so I had an extra one of those as well.
I wrote a Word .doc that described my experience with it. If you'd like a copy, let me know your email address and I'll send you it to you as an attachment. I haven't seen the Marknet instructions, but his stuff is usually good.
Life is a mortal adventure. Don't avoid all the risks.
2005 KLR650, ready for the world
1999 KLR650, badly in need of TLC...
1998 Honda Valkyrie Tourer
2001 DRZ400e, already broken... in