I'm going to eat some crow here. I'm updating this thread for completeness and accuracy. Long story short, the coolant relay came disabled on my mill. Enabling the coolant relay caused my g-code programs to stop working properly - the spindle would never turn on and engage though the coolant would. This got me down the track that they were tied together in a wierd way.
Long story short, the problem was actually in the post-processor for Visual Mill (I THINK!) where if the coolant was enabled for the tool but the spindle speed was left at the default or some such the spindle speed in the output would be wrong (it would be blank IIRC.) I didn't try and research the exact cause once I got it worked out.
The end solution was just making sure my tool library had the spindle speed set for every tool along with coolant for every tool. Instantly it all worked perfectly. The key was the suggestions to run the M codes by hand - they all worked fine as they should. That's when I realized something else was at fault.
Anyways, it's all good now and I'm still at the point where my Novakon NM-200 came from the factory perfectly set up. Simple as that.