The two big question marks in determining your trajectory are velocity and BC. Most manufacturer BC's are questionable. Bryan Litz has done some great work testing the BC's of various bullets and has published a book which will probably answer a lot of your questions.
New Book: "Applied Ballistics for Long Range Shooting"
His data has also been imported to the JBM online ballistics calc.
JBM - Calculations
This site also has a function for detrmining BC through differential velocites.
Most BC's use the G1 drag factor which is really not best suited for LR type bullets. If you can determine the G7 BC for your bullet your drop card data will be more accurate. There is an article on the in the technical articles section, again, written by Bryan.
Berger Bullets' Move To The G7 Standard BC By Bryan Litz
Velocity is the other variable which can be known with the use of a chronograph, however, not all chrony's are 100% accurate. Some may be up to 5% off. If you have a way of comparing to some other chronies you should be able to gat a good idea of how accurate it is.
When shooting at various ranges you want to record all the enviromental data, like pressure, temp and elevation.
There is more than one way to go about validating your BC and trajectories. The most common is probably by measuring your drops at different ranges. And another is comparing velocites from your muzzle to somewhere down range. You need two chrony's for that.
I'm sure someone else will chime in with some good techniques.