I have a 2014 FLHRSE (Road King Screaming Eagle).
Last fall during a rainstorm, it was parked outside. When I opened the empty saddle bags there was approximately ¼ inches of rain water in the bags.
How do I diagnose the issue w/o spending over $100 per side for new gaskets?
Is it possible that there is an alignment or fitment issue that I couldn't find?

 

Most likely coming in the bolt holes, check that those grommets are properly installed. They fit through and seal on both sides of the plastic.

 

An old trick to check how well a seal fits is to take a dollar bill. Put it so it is part way in the bag and close the lid. See if there is resistance to pulling the bill out. Go all the way around and if you find a spot with little or no resistance the seal is not pressing against the lip there. If there is consistent resistance all the way around the lid, the leak is somewhere else. If you have the one handed bags, with the lever near the front inside corner, water might be running down the shaft that goes through the bag top.

 

Over $100 per side? A set of two is less than $50 from the dealer.