Hehe, after struggling to place the head, torso and legs of pedestrians together to make the animations work in FreeSynd for the last week or so I happened to find this information about HELE-0.ANI, HFRA-0.ANI and HSTA-0.ANI. Turns out these three files contain just about everything you need to know to draw objects in the game. There are 1970 animations which are made up of frames taken from a pool of 8949, each of which are made up of elements taken from a pool of 10486, each of which index into the available 1180 game sprites. The amount of work required to manually reproduce these animations (and that I had intended on doing) is phenomonal. A conservative estimate is that this information has knocked a year off the development time. In just one day (today) I have figured out the exact placement of units on the map, fixed the drawing of animations and cleaned up a lot of very ugly code. The result is that agents can now walk around, with and without all the different weapons out, and shoot those weapons. The guards in the first level can do likewise, as well as get shot, die and bleed. I can also shoot cars making them explode.
So, again, I turn back to that great mystery of the GAME*.DAT files. In particular I still don't know where the information to place things like trees or doors comes from. I also don't know where to obtain the detailed mission objective information - like *who* exactly you have to kill to win an assassinate mission.