I ave a 3 year old Rudd Achiever Gas Furnace and have an 18 year old 2 story well that presumably was well built. Why is my upstairs 3 to 4 degrees cooler than my downstairs - especially on really cold days - since "hot air rises." All my heating registers are in the open position.

Depending on architecture you can get differences like that. The ACCA Manual D considers a 1 degree offset to be very good and 2 degree acceptable. You're not too far out with a 3-4 degree change, or there may be some air circulation/ductwork issues that need addressing. Too many possibilities to list here.

I am assuming there is just one thermostate.

What you need to do is to close down the registers downstairs about half way. What I believe is happening is the downstairs heat is telling the thermostate it is warm enough, but upstairs hasn't reached the temp u like. There might also be in line dampers near the furnace that would help regulate the heat without touching the registers.