Yeah, we'll need some more information before we can help you with a diagnosis. Need to start with the basics and the crankshaft is not the basics. You need to provide us with the year of the bike, mileage on engine and modifications (if any) to the intake, engine or exhaust system. It's also helpful to know how up to date maintenance has been (last oil change, last valve adjustment, is the carb clean, etc) and how hard you ride it (do you spend all day at 4,000rpm commuting or does this thing go to the track and average 9,000rpm).
Once that information is provided, we can then tackle the symptoms. Remember, just provide us with the symptoms, not your assumptions. A couple examples of symptoms are the temp gauge reading hot, different vibrations than usual and hard starting. An assumptions is any statement that goes along the lines of "My bike is doing X therefore Y must be the problem". While many assumptions are made with best intent, they are often not helpful and made more out of a desire to find a quick solution. In order to properly diagnose an issue, it's important to perform tests without the bias of assumption. So, to help us help you, just give us the symptoms for now.
That being said, running way low on oil for an extended period of time can cause all sorts of problems, one of which is fried bottom end bearings which will eat your crankshaft.
1990 EX500 - 139,000 miles as of April 29th, 2019
1993 Ducati 900SS - The real canyon carver
2002 EX500 - Undergoing a full restoration