VERY interesting stuff! Just this week I also had a problem with my '05 Bonnie stumbling/losing power/sputtering/etc after about 20 minutes on the road (though it never actually quit). The bike is going in for diagnosis on Monday, but after reading Mongo's and Colin's posts I ran a little experiment. First I determined if and where the seat was pressing on the igniter by smearing a bit of chap-stick on the igniter's edges. Yes, the seat does rest on the igniter proper (but not on the connector). Rather that deform the seat pan I took some pieces of a paint stir stick (about 5/32" - 3.5mm) thick and taped them to the frame where the closest rubber pads touch. The seat pan no longer touched the igniter.
Now... what does this prove?
1) The seat pan does indeed sit on and probably press on the igniter.
2) the seat can be shimmed up a bit so as to alleviate this. If I were doing it seriously, I think I would look for small rubber or maybe felt discs of the proper thickness and attach them to the seat's rubber pads.
3) The 2" (50mm) rib on the seat pan aft of the igniter does not seem to contact anything.
Now that we know that the seat sits on the igniter, it has to be determined whether this, in fact, does affect the igniter's proper operation. I have no idea how you would do this, and so I'll leave this part of the research for someone more clever than I.
Bob