On my '98, I'm able to disconnect the positive terminal and then slide the battery out to disconnect the negative.  I don't think the ground cable is original so it may be longer than stock.

I put in a new battery and it is just enough taller that I can't slide the battery in with the negative terminal connected.  The only way I could install it was to remove the seat and use a ratchet with an extension to connect the ground cable from up above.

What is the best way to remove the battery?

Also, I  added a pigtail for a battery charger.  I'm concerned, though, that the vibration could rub through the positive cable on the pigtail and short it out.  Is this a valid concern?

One more question.  The only place in town that had a battery in stock was Sears and it is a maintenance free one and my old battery was the wet cell type.  So there is now no need for the rubber tube that connected to the battery.  Anybody else use a maintenance free battery?

I went to the "Big Crank" web site and noticed that they have a list of batteries for Suzuki 650's.
Below is a discription of the All Savage battery. 1986 - 2002.
Does anyone know if this battery will fit in the S-40 battery recess case also?

Big Crank™ ETX15L Battery
Code:BIG-ETX15L
Price: $49.95

I have that same # Big Crank on the 05 S40. It was needed on such a new bike on account of I blowed 'er UP with sparks from a grinder. The stock battery( with the split case) is outside by the woodpile.