15k to 16k. Wow. Why not buy a wrecked one and take everything
I think that's what other successful swaps have done. According to what I've read, the F-150 and Mustang PCM (engine controller) is a large part of an integrated system. The system actively seeks sensor readings from other components (transmission, ABS, security) and then responds, sometime by detuning the engine for safety. Those who have successfully swapped drive trains from wrecks have reprogrammed the PCM to not look for other, now absent components.
My research indicates that the PCM is transmission-specific (but can probably be re-flashed); the computer expecting an automatic but not finding one will detune the engine. The automatic transmission's controller communicates with the PCM to aid in shifting. It seems that Ford was rather secretive in protecting the shift algorithms; this may be why third-party controllers are only now becoming available.
*** this is only what i understand based on my reading/research. I am not an expert on any of this***