You don't specify what kind of Geckos you got from Mach motion. If you are going to replace the motors, servos are the way to go, which would require the 3xx series from Gecko (I'm using the 320s). The reason for this is pretty simple, the mill is quite large to use steppers. It'll work, but they will probably get very hot given the amount of power required. However, whether you use servos or steppers, Keling (http://www.kelinginc.net/) is the best source I have found for motors. I bought three motors from them and a power supply.
As far as the spindle goes, if the current drive works, you can re-use it. The biggest problem with it is that it expects a -10 to +10 vdc signal. -10 is full speed reverse, +10 is full speed forward, with 0vdc being stop. Most of the spindle drive boards only produce 0 vdc to +10vdc, so you only have one direction. A clever circuit could swap the voltage, but no one has created one yet.
The tool changer is not that hard to deal with (see one of my previous posts for the logic and other details), but you will need more inputs that you currently have. The best way to deal with it would be a PLC, but they are not cheap, although I've recently found CuBloc (http://cubloc.com/product/01_01.php) which has really cheap PLCs. I was planning to use the Mach3 'brains' feature with a ModBus interface from CNC4PC, but Cubloc may be better.
HTH,
Chris.