1. Personal opinion, I pulled the exhaust off my 4th gen and then I loaded the tunes. I didn't Key On the truck with the exhaust off so it was never an issue. You do this whatever way you like, but if you do the exhaust first, just don't turn the truck on until you are putting the tunes on. You don't have to mess with the EGR, it's disabled by the tuning. DO NOT? load tunes and leave your stock exhaust on.
2. Yes, unplug the Throttle Valve. Buy a delete kit too.
3. This is debatable. I did not do it on my truck.
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