Here is the run down:
Step 1: Load program (My code is coming straight from hsmexpress which had worked for a couple of programs using the beta release of MSM 2.0.1 but I haven't been able to program anything with it that has worked for me since going to the production release.)
Step 2: Load probe (entering into the MDI "t99m6", Set up with tool 99 defined as the probe and master tool with the following options turned on: TC auto TCP, TC auto TLO, Skip RH tools, Master Tool mode)
Step 3: Probe corner to set zero
Step 4: Hit start and hope that the machine moves to the tool change position without triggering soft limits so that I can remove the probe and load the first tool that is being called. (spoiler alert, it doesn't make it...

below is a sample of the latest code that is giving me issues. Is it something in the code, my procedures, or is this some kind of bug?
(NOVA PEDAL 2)
(BOTTOM)
(T5 D=0.25 CR=0. - ZMIN=-0.378 - FLAT END MILL)
(T6 D=0.125 CR=0. - ZMIN=-0.05 - FLAT END MILL)
(T7 D=0.375 CR=0. TAPER=45DEG - ZMIN=-0.12 - CHAMFER MILL)
(T8 D=2.5 CR=0. - ZMIN=0. - FACE MILL)
(T17 D=0.0625 CR=0. - ZMIN=-0.05 - FLAT END MILL)
G90 G94 G17
G20
G28 G91 Z0.
G90
(FACE3)
M5
M9
T8 M6
S2300 M3
G54
M8
G0 X13.475 Y1.0225
G43 Z0.605 H8
Z0.205
G1 Z0.1 F40.
G18 G3 X13.375 Z0. I-0.1 K0.
G1 X13.25
X-1.25 F80.
G17 G2 Y2.9525 I0. J0.965
G1 X13.25
G18 G2 X13.35 Z0.1 I0. K0.1 F40.
G0 Z0.605
G17
G28 G91 Z0.
G90
(2D ADAPTIVE4)
M5
M9
M1
T5 M6
S2300 M3
M8
G0 X0.2508 Y-0.1885
G43 Z0.605 H5
Z0.205
Z-0.353