Just in case it could be helpful, here is the full method that I had written up earlier. The emphasis here is for the three contact points of the finished bike, but the method can be supplemented for stack and reach measurement by adding in the distances vertically and horizontally from the BB to the top center of the head tube. I realize you have already done this, but others may like to see the full writeup. I was away from the computer before and didn't have a copy of the Word file to paste in here:

The way these measurement are done is not in relation to each other, but in relation to a fixed point in space. It is much easier that way as you don't need to use a level, plumb bob, or other tool to make sure you are not making a mistake. Here is how it is done:

You first inflate your tires to normal pressure. Then using supports or a trainer stand or an assistant place the bike with its rear wheel against a wall and perpendicular to it. The bike must be perfectly upright and not slanted to either side.

Then you make six measurements:
A) Wall to center of bottom bracket horizontally.
B) Wall to front tip of saddle horizontally.
C) Wall to back edge of handlebar center horizontally.
D) Floor to center of bottom bracket vertically.
E) Floor to top front of saddle vertically.
F) Floor to top edge of handlebar center vertically.

Now you have everything you need to relate the three contact points on the bike to each other. A-B gives you the saddle setback relative to the bottom bracket. E-D give you the height of the saddle from the bottom bracket. C-B gives you the distance horizontal distance from the saddle to the handlebars. E-F gives you the drop from saddle to bars.

Done and done.