The IR image is 640x480 and the visible image is 4000x3000 pixels. When yr merging 100's of images together these sizes are good. Its true that the IR maybe too small for some programs but I'm told its ok with Maps Made Easy. Probably why DJI brought out the Advanced with a larger IR sensor.
I think my biggest issue was a fouled memory card. I have a new one and it seems to be working better. I need a few more attempts to replicate my previous successes before I'm confident to move it into our SAR ops. One workaround I did do was a direct download out of the M2ED to Pix4D that worked fine. I'll let you know.