@Phaedrux a quick update, I commented out the T-1 at the beginning of my t0pre.g that I added in, and it is now working. I guess that is causing confusion in the printer, just added it in for safety and forgot about it. Problem solved!
t0pre.g
; tpre0.g
; called before tool 0 is selected
;T-1; deselect any tool currently held
G29 S2;
M568 P0 A2; set tool active.
;Unlock Coupler
M98 P"/macros/Coupler - Unlock"
;Move to location
if move.axes[1].machinePosition > 200
G53 G1 Y200 F50000;
G53 G1 X-5 Y200 F25000
;G1 Y205;
;Collect
;G1 X-10.5 Y242 F2500
G53 G1 Y225 F2500;
;Close Coupler
M98 P"/macros/Coupler - Lock"
;WARNING! WARNING! WARNING! WARNING! WARNING! WARNING! WARNING! WARNING! WARNING! WARNING! WARNING! WARNING!
;if you are using non-standard length hotends ensure the bed is lowered enough BEFORE undocking the tool!
G91
G1 Z10 F1000
G90
M116 P1; wait for temperature, this will not wait for temperatures above 40C.
;Move Out
;G1 X-10.5 Y150 F4000
G53 G1 Y150 F4000;
G29 S1;