I ordered the Triumph workshop manual when I got my Scrambler about a year ago, I was presented with the 2004 version too. No Scrambler specific stuff in it, although the bonnie and Speedmaster pages cover most of it.
Yesterday I pulled the primary drive cover to polish the lacquer and corrosion off, the crankcase breather is different from other bonnies. Earlier bikes have a metal pipe in the case that joins the crank end to the breather hose, on the Scrambler it's all hidden under a plate behind the clutch sprocket.
If you want to save a few bob you can have my '04 manual, pm me your address. I put alloy rims on mine btw, Tiger front and Thruxton rear. I already had the front, left over from super-moto'ing my Tiger, but had to buy the rear from Triumph. Cost Â£260, I couldn't find any s/h Thruxton wheels.