If I was doing a fuel swap I would have the tank out of the car and get as much petrol out as possible, then dump 10-20 litres of diesel into it. As it's not a super-advanced TDI it'll tolerate a *little* bit of petrol, but really removing the tank and dumping the fuel out the filler is your best option to clean things through.
Make sure you're running the correct diameter pipes to and from the tank, too - IIRC carb G2s have smaller diameter return lines - what size were the G3 lines? Equal?