The gen1 midpipe bolt pattern where the muffler bolts on is the mirror image of the gen2 midpipe. BOLT ONS, not slip ons, as slipons come with there own midpipe(alot of slipons will interchange with little to no modification too).
So gen1 bolt ons will bolt to a gen2 if you switch the sides of the mufflers; and they must have sliding mufler hangers(as most aftermarket mufflers do). Stockers won't directly swap because the muffler mount hole is fixed, and the gen2 is a couple inches further up the muffler than the gen1.
Gen1 and gen2 oilpans are also shaped differently(bolt pattern is the same).
Gen1 and 2 header tubes will fit either gens head, but depending on the header brand you may or may not have oil pan clearance issues with the bend under the pans.
Handlebars interchange, and Heli-bars interchange, but you will need to drill new switch housing locator pin holes. As the switch housing spacing and orientation is slightly different between the gens.
Mirrors also interchange, as well as with gsxr1000 mirrors from 01 up.
The 600/750 mirrors from 02 up are also the same.
Frames are the same, with one exception. The gen2 has one extra hole on each top side near the front of the gas tank. The holes are for a plastic pin that helps secure the gen2 fairings
Aftermarket rearsets will fit either gen.