Jake,
If you want a set of the Lionel cars, Trainbuddies (www.trainbuddies.com) has two sets available - West Side Lumber and Western Maryland; on their site search on Skeleton. The Trainbuddies are great guys to deal with - I bought a set of the log cars myself two months ago.
Also, Atlas Industrial Rail is making some nice skeleton cars.
I know you were asking more along the lines of building cars but thought you may want to know of some sources in the event that you can not get what you want built.
- Luther
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