All the stator bolts are the same. It doesn't make a damn bit of difference where they go. The two bolts that hold the shifter bracket on the gear cover are longer.
I struggled with the "nagging oil leak" (search that here if you care to) for months. I tried everything and had the cover off and on again about 10 times. I tried gasket only, gasket+sealant, sealant only, different kinds of sealant, double gasket, NOTHING worked. After the motor got hot and was parked, there'd be a spot under it.
What finally cured it.....the cover was warped. Note....the bike didn't leak a drop prior to me having to replace the stator, and I'm pretty sure I broke the "factory seal". The cover was not particularly difficult to remove nor was it excessively pried on. But when I finally put the cover on a known flat surface, it had a noticeable "rock" to it....it didn't sit flat. Same story for the middle gear cover.
I took both covers to the big 24" disc sander in the student shops and just pressed them up against it. Very quickly "low" spots appeared that weren't getting sanded. I kept going until the surface was uniform. Cleaned them up, used a new gasket for the stator(added a bit of threebond/yamabond on the bottom to be sure), and used only Yamabond for the gear cover. Bone dry since then.
So find a way to sand the covers flat again. I also took a little off the gears of the reduction axle, to ensure that because the cover sat slightly closer now the axle wouldn't bind up. A big disc sander worked well, and the little 4" wide bench sander at home worked fine also.