Need help on welding cylinder head

[Ron66]

I recently picked up a small 50cc mini chopper. One of the exhaust studs was broken in the head. I removed the motor and tried to use a bolt extractor but the extractor snapped off in the bolt. I went a little extreme and cut the flange in the casting so half the bolt was exposed and knocked it out. Now I want to tig to build it back up so I can drill and tap a new hole. So now the questions...
1. Should I leave the motor together or take it apart? I'm inclined to leave it together since it will most likely warp less.
2. I'll need to manage heat. I've seen Jody do this in videos with a non contact thermometer. I have one. What should my target heats be? How hot should I let it get and how cool before I start welding again?
Any other advice would be helpful. I've welded lots of cast aluminum but never on a head. Thanks in advance!