You just need a couple of stepper motor drivers, a laptop or any PC running dos and a copy of turboCNC (free to try).
http://www.dakeng.com/turbo.html (download it and read the readme to see how simple it all is)
Say your lumps of wood are quite heavy you might want to use a decent sized stepper motor so a
www.geckodrive.com would suit well, you also need a powersupply and a parallel port cable. You then just write a very simple program in gcode to do what you suggest. You don't need an encoder as the motors will move the axis by a given amount with each step. The spindle can likewise be moved down to the required depth and back up again.
You would probably add homeswitches to find the zero of both axis, this could be done at the start of each cycle or just at the start of the day.
If you have not seen g-code before
G00 X100.0 F100
Would move the x-axis which might be your wood moving axis by 100" at a speed of 100"/min.
There is a similar command for a drill cycle and you just retract the spindle by the same amount it plunged. Then another G00 command to move to the next hole, then another drill cycle etc. Finally move back to the start, you can add a user interupt command so the user can load the next plank and then press go.
So now I have saved you nearly $10,000 can I have the change
Graham