As BigblackGS says, while you may be able to get the drive shaft off with the swing arm in place, it would be very difficult (or impossible) to refit it - at least that was my experience on my 1100.
So, if you haven't done it already than take the swingarm off - it's only another couple of pivot bolts to heat and remove (just like the paralever pivots you've already removed).
Assuming you're looking at the drive shaft hanging off the gearbox output shaft with no swing arm round it (like this):
<a href="http://picasaweb.google.co.uk/lh/photo/xjCau9d77xHBoc2pHOwuUw?feat=embedwebsite"><img src="http://lh5.ggpht.com/_SSn2CtCOKnU/ScdTt3eeU3I/AAAAAAAABYU/NH6gbCIWtVs/s800/13.JPG" /></a>
can you feel / see any back and forth movement when you grab it and push / pull? There should be some as it's located by an internal circlip which locates on a slot machined into the output shaft - you can just about see it in this pic (not the best photo - not easy taking picture with you head wedged half way up the back of the gearbox!):
<a href="http://picasaweb.google.co.uk/lh/photo/3vkJwrps7GdQ0c7l4jcG3A?feat=embedwebsite"><img src="http://lh6.ggpht.com/_SSn2CtCOKnU/ScdUAs5YmlI/AAAAAAAABaI/TqqI72QQcow/s800/IMG_4342.JPG" /></a>
This circlip is a fairly sloppy fit in the groove so allows noticeable movement (to the point when it can scare you into thinking you've got a knackered output shaft before you realise it's just the circlip - DAMHIK

).
If you can feel this movement then it just needs either levering out with something in the UJ or firmly hold the shaft with both hands and give it a sharp rearward pull (this worked for me both times I've done it).
If you can't feel the movement the it may be be seized onto the output shaft and you've got a tricky job on your hands. This is outside my experience but I'm sure others will have been there and will be able to offer some advice.