Hi eck, I have a 2001 Y reg KA. I have had a look at the wrench and jack and it is quite simple.
To fit the wrench back into the jack, fit the slotted end of the wrench into the slot on the foot of the jack and then fit the other end onto the top of the jack where there is a slot. You can bend the foot of the jack back to allow you to do this, once it is in, the foot will spring back.
To fix it back into the boot you put the long screw through the circular hole in the centre of the shaft of the jack and then turn it by hand into the hole on the side of the boot. I don't know what you mean by hexangonal screw as the one I have is just bend over at the top to allow you to screw/unscrew it by hand. Hope this helps. Maybe it's different on your model but I wouldn't have thought so as this model has been pretty much the same for the last ten years. Let me know how you get on or if you have any queries with these instructions. You've probably figured it out by now anyway :-)