No, the oil pans are different. Not to say it can't be done, but it won't just bolt on and line up correctly everywhere. Depending on what mufflers and midpipes you have also matters. Some of them won't just bolt on, the combinations vary.
The stock gen2 header also has a catlytic converter and O2 sensor bung in it. The convertor can be gutted and the bung welded up.
If you have a trashed gen1 header on a gen1 Busa, a good gen2 header, welding skills, and don't want to spend any money, then it's a good idea. Otherwise I'de keep what you have or buy something new.