The old transformer had 4 wires different colors. New Honeywell AT72D has Primary BLK-COM, WHT-120V 50/60Hz, and two screws on the load side with an R and C. I thought it would be obvious, but it is not to me. Do I have it right? PR1-BLK, PR2-WHT Secondary I am not sure which should go where? SEC1/SEC2 R or C?

Thanks

Here is the installinstructions:

http://customer.honeywell.com/techlit/pdf/60-0000s/60-0428.pdf

You failed to say what colors the old transformer had. If it had a white and a black connected to the primary side, white and black are appropriate.

The red and orange wires should each have a wirenut placed on the ends (capped).

The secondary phasing only matters with newer furnaces with flame rectification flame proving systems. In which case, an error code will be set on the control board. No damage will result.

Primary colors on the old were Black - PR1 and White PR2 and Secondary colors were Red for SEC-1 and Blue for SEC-2 My furnace is at least 20 years old, so it should not matter where SEC wires go. Thanks for your answer.

Yep.