Speeds & feeds are a pain! I watched burning embers come off of mine once Usually its from going too slow, or a dull bit. I have multiple fire extinguishers in my shop.
It can get frustrating "wasting" time in front of the computer, when you could already have a neck done by hand in the same amount of time. I spent almost 2 years (and a lot of wood) figuring out the best way to approach my CNC'd necks. Half of that time was spent trying to get the 3D model the way I wanted it. The rest of the time was experimenting with machining operations. In my case I found it's best to leave a small amount of "sanding stock"...usually .010" to .020". Smaller CNC seem to have a certain amount of deflection due to their size, which may be why yours is off a few thou.
What I settled on was laminated necks with no scarf joint...which can be a selling point. The Jackson CS charges extra for no scarf. And, I find they are very stable. I make my blanks 3" x 36" which yields 2 necks. It comes out to less than 1.5 BF per neck. If I didnt have a 13 degree angle on the headtstock, life would be much easier, and I would use less wood. As far as the number of actual operations... I havent counted. I do them in batches of 12, so all of the roughing is more of a production. When I schedule a build, I pull from the roughed in stock, slap it on the CNC, and hit "start".
It actually helps to do the TR channel before the CNC. Get some .250" x 1" ground dowel pins from Granger. Pop three .248" dia. location holes about 3/4" deep in your spoil board that are centered in your neck model. Then, use the tr channel to seat on the pins when you machine the neck profile. It will keep the blank centered on the TR channel...."Pins are our Friends"
Here is a recent video I did of the process:
http://www.youtube.com/watch?v=7eUKrZsASQc&feature=g-upl&context=G2740dccAUAAAAAAAAAA