I'm with SWAG. Print a 1:1 transparency of your stencil file and mark it where you want to place the pins. Place it in the product file and use it each time yor run that product. 1. Get the pcb into the print position. 2. Tape your transparency to the conveyor rails so it matches the pcb. 3. Remove the pcb 4. Place the pins under the transparency. 5. Remove the transparency and run.
As far as rev changes to the pcb go - if you have to fab a new stencil - print a new transparency, it'll cost you all of 50 cents. I won't have a stencil made in the first place until I've matched the pcb to it's transparency.
Search the fine archives - I think you'll find many people have "issues" with the grid and RED-E type systems.