Sorted it finally, I had the switch on the cable the wrong way round.
It should be pushed towards the right.
So all I did was the method outlined in my previous post on page 8, then:
Once you have prepped winkfp with the e89 daten, just select comfort mode-> update ECU-> EMF89 Unverbaut-> Done-> Prog.ZB-Update. No need to enter VIN or ZB number. It will then read the existing software version from the car and show the new software version and ask if you want to update, so obviously say yes. Takes about 5-10 minutes and the parking brake will come back to life. Cruise control also working now too.
Also no need for an external power supply, just put the key in and press ignition on, without engine running. Battery SOC did drop from 56% to 33% though, so best to do it on a 'hot' battery I guess.