Your choice isn't bad at all. The F150 and the Mustang Coyote are mechanically identical except for the intake cams, 1/2 point down in compression and a different intake manifold.
The controls pack for the Coyote doesn't look as friendly as for the LS engine but, it is available, if not particularly cheap.
Pretty sure the intake manifold is the same. The truck motor doesn't have the integrated windage tray gasket the Mustang version does.
The front cover is also different.