In long, for a full numbers matching it means all the parts on the car came with that car from the factory, frame, fenders, pretty much anything that bolts onto the car with a stamp on it... whereas Pontiac did a horrible job of keeping records and documenting various things.... the main items for a numbers matching car is what Renovations said, engine and transmission.... the frame is stamped as well but in order to see the stamp I believe you have to have the frame off the car....
Seems like you are doing things right, as finishing it right the first way may take longer but you know its done right. I am doing the same thing on my car, and want it done right. Its been 6 years and its finally coming to a close! post up some pictures of what your car... EVERYONE here would love to see it.... and never be hesitant to ask any questions or look for advice. Lots of greats people on here....