Ok, I've gotten way too far into this now but I just love the Alfa
After clearing the codes on the ECU, I drove it for 5 miles then checked the fault codes again - none. Then I found the Idle Reset option in AlfaDiag and ran that, then did the 90sec off, 90sec on trick on the key. The idle problem has improved big time and the car is much better. Its still hunts to 1500 when I push the clutch but returns to 850-1000 in seconds. Drove 250 miles, no fault codes! And no stalling
I thought this might be helpful for others out there, battling with the cable/software problems.
I've got the air bag light on too, so I downloaded the KWP71 software and modified the cable. To be clear, you can simply solder a wire from pin 7 (main ECU) to 3 (air bag ECU) by bridging/shorting the pins). You can do this because the ABS, Airbag and Main ECU are all separate ECUs and you connect separately to each one at a time in Alfadiag (i.e. Main ECU - connect to Motronics 1.5.5, Airbags - connect to MY97). This worked fine (and took 10 minutes).
Also, for those using Win XP, you can change you COM port assignment. My PC auto selected COM9 for the USB VAG cable. If you click start, right-click MY computer, click Manage, then expand Device Manager, expand COM & LPT ports. Find the only USB COM port listed, right-click select properties. Click on the Port Settings tab. Now, if your using KWP71 the max speed I could get was 4800 so on the port settings tab make sure Bits per Sec are 4800. If you want to change the port number (in my case KWP71 had a COM range to COM8 so it couldn't see my COM port) on the Port Settings tab, click Advanced. On the advanced page is a Com Port number dropdown list. Select a COM port number as low as possible - or at least lower than COM9 so KWP71 lists it. You shouldnt need to change any other COM port settings. I found KWP71 a bit buggy and it disconnected a lot, although this might be a problem with my Air Bag ECU. Once you've change the COM port settings, open KWP71 and select your new COM port number, prot sub type = KWP81 ??, ECU = 0x00, leave all other settings as default. Now click Open COM port, then click Start Com. You should be able to read your fault codes, click on read faults.
I then connected to the air bag ECU using Alfadiag. Once Alfadiag has started. select MY97 from the ECU list to connect to - it may fail to connect. This is because the COM port you select is per ECU in the list to connect to. Therefore you need to go to interface and select the right COM port (especially if you changed to the COM port number using the method above).
Now, Alfadiag has an air bag fault code of 0000 - ECU intermittent fault. It also registered Crash 1, 2, 3, 4 in the System Snapshot data. Does anyone know what that it? Is this part of my problem?
I hope this helps someone else :-)