Sandy, there might have been some mild armoring such as steel plates inserted in the panels and trunk to surround the back seat, but for the most part it was probably stock. The White House used a lot of stock cars before the Kennedy assassination, especially for short distances that weren't deemed a threat.

Even the Lincoln X-100 that Kennedy was shot in had limited armoring. And, many times on trips he and Johnson were driven around in stock Continentals borrowed from local dealers so they didn't have to get the big car out, even on their trip to Texas. That changed after November 22, 1963.

Here's some articles on a '55 Cadillac limo that was modified for parade use:
http://blogs.wsj.com/drivers-seat/20...imo-next-week/
http://www.carbuzz.com/news/2012/12/...ction-7712189/

A funny story about Ike and cars: when he was getting ready to leave office in 1961 he realized that he'd forgotten how to drive. He hadn't driven a car since he became NATO commander in '51. Those 10 years and the stroke he had in '57 made him forget how. He worried that retiring to his farm in PA he needed to learn to drive again. So, some Secret Service agents thought it'd be easy since cars now had automatic transmissions, power steering and brakes. They took him to the WH garage and after a couple of hours he just couldn't get the hang of it. Finally, he got out of the car, blurted some cuss words, and said, "I guess Mamie will have to drive me around!" He then ordered her a new Plymouth Valiant.