I have in the past been involved in a couple of projects that are very similar, one just recently, a tube cut-off machine, and the other angle punch involved in the production of HydroElect-transmission Towers.
Both incorporated some of the ideas you have mentioned.
One thing I would comment on is if intend doing any kind of Mill/drilling as you suggest, Is to have some kind of clamping vise arangement when stopping to perform the operation. At this stage the servo action of the motor should be turned off but the encoder still monitoring the position. There are commands in some controllers that allow the turning back on of the servo and assuming the current position as valid, so that the motor does not jump to cover the assumed error.
The first project I mentioned, used a servo operated carriage to push the part through the operation stage, The start end of the material was detected by photo-cell detection.
The second was a air/hydraulic pusher that had an encoder on the pusher just for measure reference. Both operated on 25'~30' material.
Al.
CNC, Mechatronics Integration and Custom Machine Design
“Logic will get you from A to B. Imagination will take you everywhere.”
Albert E.