Here is what I have come up with so far. I have been running test prints with no filament using this in the post process window:
{REPLACE "; layer 3," "G91 \nG1 Z10 \nG90 \nG1 X0 Y200 \nM400 \nG4 P180000 \nG91 \nG1Z-10 \nG90 \n; layer 3,"}
This works.......sometimes. I determined by testing different M and G codes for pause that the buffer is causing issues. The G4 would work but always after the head moved over and came back to resume the print then it would pause for the dwell time after the buffer was clear. (Strangely only P dwell seems to work not S dwell).
M400 makes it pause where I want it to, gives me three minutes to do a manual filament change and then it resumes the print after the dwell time. Here is the funny part. Sometimes is resumes and completes the print, sometimes it resumes for a short time and then starts doing crazy things like moving over to the edge of the bed and then coming back. One time is seemed as though it completely started the print all over again by moving the head down to first layer height and running the start G-code. I know this cause it did a nozzle wipe which is only in the start G-code. This weekend I'm going to save my G-code to SD and edit the line above at the correct layer start and see what happens.