2 wire is for turn signal only, 3 wire is for turn and running lights. Can't say for all Buells but I know my (2003 R) XB has only 2 wire for front and rear. I have these on the front. For the rear I got a NOS led inserts for a Sportster from the local HD dealer for cheap on the NOS table and put them in the stock housings with some filing of the led inserts. I wired it so the rear turn signals are now brake and running in red and turn in amber. I really just wanted to have more then 1 rear light for running and brake. Note you will need an led flasher relay or you will get hyper flash. Got more questions let me know.

Like you said HD dealers seems to be a hit and miss with Buell parts. If you are ok with used I would go with ebay but you can still find new parts on there, or check the classifieds on badweathernikers. I am going to guess a different make or universal shift pedal will be more work then what it is worth. As for turn signals I would avoid the super cheap ones and aim for $45-60 for front and rear. These https://www.amazon.com/dp/B00BLPRMYA/ref=cm_sw_r_awd_LSuWvb6YXKHR2 you will need a LED flasher to go with them.