One of the old Airhead gurus, Das Snowbum, will tell you to carefully dress out the ding so that the cylinder can be refit without excessive force. Note the cylinder's base has a large diameter o-ring that seals the crankcase joint. There are also two small o-ring for the upper crankcase stud, but that's another story.
Rods are hard steel. Seriously doubt that they/it incurred and damage. If you visually inspect the rod, it may even be difficult to find the point where it made contact with the crankcase.
Strongly encourage y'all to purchase the Clymer and Haynes service manuals for your new-to-you Airhead. Read up on what chores you wish to accomplish prior to jumping in. These are basically very simple machines but you really want to avoid that
Oh, S#*t moment when you discover a serious loss of $$$ and time.
Bob "Snowbum" Fleischer is a treasure of Airhead knowledge. His technical articles are extensive and detailed. They can also be used as a fast cure for insomnia.
http://bmwmotorcycletech.info/From your photo, it appears someone in the dark past of your R65LS has used some sort of sealant when the pushrod tube grommets were installed. Clean out the remnants and do not repeat this error.
Welcome to the herd and our own little BMW asylum. We cannot offer a 12-step cure for the "addiction".
