Today, I spent some time getting familiar with Target 3001 as a test drive. It seems very functional and able to do board design. I did like the part search feature that narrows down the search based upon component package and size. My biggest concern is the fact that most of the aspects of the program are geared for european countries, including the package library. While this isn't the end of the world, it does pretty well ensure that I'm going to be forced to design every part. Of course, I'm already well versed in designing parts in Eagle.
I also put the finishing touches on my EMC2 controller installation. Once it all looked good, I dragged it downstairs into the workshop and hooked it up where the Mach3 machine used to be. I put EMC2 through its paces and everything worked perfectly. I had added two features to the base installation which is the PCB height mapping python script and the Z-axis auto touch off plate with the probe. Both worked perfectly as well. I had my little Zenbot tapping away on top of a blank copper clad board as it mapped out the surface for any high/low spots.
So, with the pros and cons of both approaches, I think I'm going to go the route of simply replacing my Mach3 software with EMC2 and continue down this path to get PCBs milled. I still need to actually run a real job with the new EMC2 control computer and software to be sure it can do everything my Mach3 installation was doing with as much quality. So far so good though.