>It does find the mmc3 but I have to clue what it is waiting for. UTP?
"waiting for. UTP" means that there is no communication channel through usb.
Is board working fine when programming with mfg tool other devices, for example sd?
Also one can check if mfg tool is starting correctly: just click mfgtool2-yocto-mx-sabresd-sdcard-sd4.vbs
script and tool will start with all necessary parameters.
regarding "mfgtool_output.log.zip" - I noticed that you used Linux version 4.9.88 for it.
Note mfg tool package is linked to appropriate linux kernel and files in L3.14.52_1.1.0_ga-mfg tools
can not be replaced with files compiled with L4.9.88. Please look at link below
and use Linux version 4.9.88 Mfg Tool for files compiled with L4.9.88:

i.MX Software|NXP
the same is valid for Android- for example latest Android O8.0.0_1.0.0 is based on L4.9.11 GA
according to Release Notes included in Android O8.0.0_1.0.0 BSP Documentation
and only L4.9.11 GA should be used for compilation new mfg tool firmware.
