Hi there,
I believe you will need a 44 pin IDE to 40 pin IDE convertor cable to plug in your CDROM, but if you want to run the HDD as well, you should get a buffered IDE interface from Amikit, which will allow you to connect the CDROM and HDD together (The Amiga has only one IDE connector inside it). You can connect two devices (Master and Slave) on a single cable to the one IDE interface, but it's not recommended (and something gets very hot, processor I think?

, can't remember, long time ago ). :-?
I have recently been buying Joysticks secondhand and have found that most of them haven't worked when I tried them. I have managed to fix all of them and they all so far suffered from dirty contacts inside the Joystick. A little bit of contact cleaner and a cotten bud goes a long way I have found.
I remember you saying you had the Joystick plugged into a Joystick/Mouse swapper. Have you tried the stick direct?
Do you have only one Joystick to test with or have you tried other Joysticks?