Despite recovering from the tragic plane crash, many other issues affected the bassist's health in the years following. On tour in the early 1990s, Wilkeson was rushed to the hospital after his throat was cut while he was sleeping by someone on the bus. He survived the incident, but the perpetrator was never identified, according to Rock And Roll Paradise.

In 2001, he was cited for driving under the influence in Florida, a charge he was preparing to face in July of that year when he was found dead in a room at the Sawgrass Marriott Resort & Beach Club in Ponte Vedra Beach, Florida. According to the report posted at Autopsy Files, Wilkeson was suffering from emphysema and cirrhosis of the liver at the time of his death, with drug intoxication as a contributing factor. A medical examiner subsequently ruled that Wilkeson suffered from chronic lung and liver disease and died of natural causes at the age of 49, per Billboard.

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