1. Use a complete MK2 kit, except the pump. Run the MK2 PAS pipes to the MK3 pump
2. No, use the old flywheel, and a new MK2 8v vlutch, the 2e flywheel is heavier than your old one!
3. Use a 2e alternator if possible, the MK2 PAS bracketry is total rubbish, so stick with the MK3 setup if you can.
If you keep all the standard 2e bits on the bottom end, you'll need to fit the 2e front plastic coolant flange as the pipes from the waterpump etc are different. You'll also need a 2e metal water pipe as well, and you'll have to block off the header tank overflow pipe on the rad with a short length of hose with abolt threaded in, as the 2e flange has the header tank overflow on it.
This is the end result of my 2e bottom end conversion, I tried to use as many 2e bits as possible:
