Sounds like the guy (or gal) saw something strange and assumed that your vehicle did not meet some regulations. There is a definated hierarchy of regulations that need to be understood...
FMVSS (and CMVSS) - Federal Modor Vehicle Safety Standard (and Canada MVSS): These documents provide the MINIMUM guidelines for vehicle requirements. When an issue is not defined in SAE or state regulations, FMVSS is referred to. It's broken up into 4 categories - Crash Avoidance, Crashworthiness, Post Crash Standards, and Other Regulations.
SAE - Society of Automotive Engineers: Provides documents to further define requirements and test standards that are used to help engineers design parts and systems. SAE standards will refer to a specific FMVSS section.
State regulations - Each state has the authority to further specify requirements beyond FMVSS and SAE.
Sooooooooooooooooo...
The cop must have had an issue with FMVSS 214 - Side Impact Protection. I have to read through the standard to find out if there is something that you can fight with. However you have to check with your local laws that coincide with the 214 standard and specify further requirements.  

o you have nerf bars or any other side protection? This may be very important in your case. I'll hopefully give you good news soon.
Windshield folded down...
That one falls under FMVSS 111 - Rearview mirrors. I believe that the GVW stamped on the plate of my vehicle states a weight of 4650 pounds (for my '79 with a hard top). That barely makes it into the section S7 (vehicle weighing between 4,536 and 11,340 pounds. You are only required to have outside rearview mirrors on both sides. You had to be wearing glasses though because of the requirement of having a non shatterable media between your eyes and the road.