You got lucky.
In particular reference
http://www.nhtsa.dot.gov/cars/rules/import/FMVSS/
and
http://www.fmcsa.dot.gov/rules-regul...ection_toc=777
Check sections 206 and 214 in particular and 201 to a lesser extent.
You could very well be cited for modifying your doors and would, in court, have to justify your modifications based on FMVSS statutes in effect either at the time of manufacture/first sale or at time of modification, whichever is the most restrictive of the two.
There are also kind of 'lazy laws' which allow an officer to cite a person based on the officer(s) personal opinion of the safety or road-worthiness of a vehicle. Also many states and localities have laws requiring something to the affect of: if it came on the vehicle at the original time of sale, it must be on the vehicle and in operational status and if it's not, it must meet the standards in effect at the time of modification or retrofit.
For those complaining about Jeeps, if the door on the Jeep provided no significant protection to the occupants, not having the door has no negative effect on the safety of the occupants when compared to the factory door. Also, the half-doors on Jeeps are sold as a manufacturer option which would have gone through testing and found to not negatively affect occupant safety.
Toyota never tested half-doors.