Here are the steps I followed:
1 Manually modify drill file code for x0 & x1 (0.125") to be -0.31" deep (z-axis) (0.25" + 0.06")
2 Tape edges of PCB material to spoiler board
3 Zero X0 & Y0 where Left Pin Hole will be after drilling
4 Run Drill File, using 0.03125 end mill for all but 0.125 holes
4.5 Run height mapping python script with top etch file.
5 Run top etch file using 45deg taper PCB bit
6 Flip board in X axis
7 Using 0.125 alignment pins, line up holes in PCB material with holes in spoiler board
8 Tape PCB material to spoiler board
9 Remove 0.125 alignment pins
10 Jog to x1, re-zero x axis at x1
10.5 run height mapping python script with bottom etch file.
11 Run bottom etch file
12 Run bottom Mill/cut-out file using 0.03125 end mill.
Broken off carbide end mills make great allignment pins. They are exactly 0.125" inches around and fit the alignment holes tightly, when you drilled the holes with a 1/8th" bit that is. The only thing is, they are really way too long and stick up. I tried to cut one down shorter earlier today with Dremel tool cut-off disk. The carbide end mill shank just laughed at me and thanked me for giving it a nice shiny polish in that part. Needless to say, I didn't get them cut. That is why I use them to line-up the board to the spoiler board below, but remove them after I have secured the PCB material with tape. The trace isolation program does in fact stop at each hole and mill them out, so if you had a pin there near the height of the board, it would break the bit I'm sure. I later read that you would need to cut carbide steel like this with a diamond blade.
EMC2 doesn't want you to insert a tool that is a different length than the one you started with. So, when it prompts to change tools and you put in that really long end mill that needs to be re-touched-off for height, you gotta manually stop the program, get the z-axis re-zero'd. Once that is done, you gotta scroll down your program, right click the next line that needs to be executed, and tell EMC to "execute from here". This bypasses the first part of the file and keeps you going. My component hole drill bit overall length was much shorter than my hole alignment bit, causing this issue.
Before running the height-mapping software, be sure to properly attach your probe and ground the top plane of the PCB material to get the probe to work. I forgot to do this part...always time to do it again if you don't do it the first time :p
The height-mapping script maps the whole area, including the place where you have already drilled holes. It actually starts at x0y0 and trys to jog down inside the hole sitting there. I had to trick the probe by using a jumper wire to prematurely short the probe and cause a reading, even though the bit didn't actually touch the surface (since it was sitting over the top of a hole). I'll need to figure out what to do about this to make it right and not trick it to get a fake reading. I'm sure this affects the output of the program by giving a non-exact reading in this area of the board.
Be sure your spoiler board is big enought to provide support after you flip the board over. In my case, part of the board was hanging off the spoiler after the flip. This caused a shallow milling on the back-side of the board due to lack of support. I think it will barely be OK, but it doesn't look quite right.
Views of the board from front and back. Diameter is 1.25 inches
Board layout view from Eagle: