From another web site I researched saddle height:

You contact the bike in 3 places....saddle, pedals and handle bars (say the tops to keep it simple).

If you are comfortable on the T-1000, take the measurements from the saddle top to the pedal spindle with the crank arms at the bottom of the stroke (crank arm parallel to the seat tube), and from the tip of the saddle nose to the center of the bars where they are clamped in the stem.

If you are also interested in 'bar drop' (distance from the top of the saddle to the top of the handlebars from the top of the saddle), set the old bike up so it it level, and measure from the floor to the top of the saddle, and from the floor to the top of the handlebars. If the bars are higher, you have 'negative' drop, if they are lower, you have positive drop. As you can tell from the racer pictures, some of those guys have huge positive drop.

I use about a 12" square piece of 1/4 plywood I had laying around set on top of the saddle and measure from the bottom side of it to the pedal spindle.

Transfer these measurments to the new bike as close as you can. This will at least let you set up the new bike as close as possible to the old one, and then you can go from there, changing stem length and/or angle if you want, removing steerer spacers if you want and changing stems and the angle of the drops and/or brifter position.

As far as a stem length and angles....I worked up an Excel spreadsheet that will calculate the 'reach' and 'height' of various stems, so I could compare changes.

I did a similar thing earlier this spring...wanted to extend the reach, but not change the height much, so after re-visiting some trigonmetry functions and testing them, I figured out a spreadsheet.

If you have Excel, PM me and I will email you the spreadsheet.