If changing the rear fender takes too much mechanical inclination, you may wanna think twice about taking off the sissy bar, if only for the reason that when you do, you'll be left with a bunch of random holes on the sides of your fender (8 to be exact) and you'll be missing your rear turn signals. You could just pull the sissy bar up out of the housing that holds the turn signals, but it would probably end up looking like a bike with a missing sissy bar rather than a bike without a sissy bar (if that distinction is clear). In other words, it would probably look somewhat hacked and accidental. As for the pillion, thats not really something im familiar with, but im sure the other guys can help out.

Of course, if you got the sissy-bar-less rails from a newer Boulevard S-40, the bike would look a lot better.  Where would you find those?  From someone with the newer style who [i]wants[i] the sissy bar so he can mount a luggage rack!  I swapped mine out, so I don't have them any more, but I'm sure there's someone who has them just lying around...

Or, you could just remove the pillion pad.  It's just two screws after you pry off the "Suzuki" tag on the back.  It's just held on by sticky tape and can be re-mounted if desired.

Here is how I did mine. After rerouting the taillight wires and installing the bullet tail lights I only had two holes on each side to deal with. I used 3/8" chrome plugs from Lowes to plug them.  

http://www.model-t-man.org/Savage/SavageHDSeat.JPG

I've often wondered if the sissy bar is better off for safety reasons?  In an accident if you slid backwards with force and nailed your back on the sissy bar as you were thrown off the bike, seems to me you could damage your spine?