After you fight to remove the top bolt to install the right side notch the top hole and install bolt and washer just snug to install loosen it enough to slide fairing in and tighten.I discovered this gem when I did my rocker lockers and zero room. This was my fix to the problem. Use the factory bolts as the junk hardware they send is laughable. Use factory hardware.

 

Funny. I just installed set from Hogworkz. Their instructions were written by a 5 year old. Same as you, I thought the bolts were too long, but I just kept turning it and finally they went all the way. Quality is pretty good too.