Ferms thoughts were going to be echoed by me but I understand, you got the sickness..
Sort out what you can when you can so when the boat is done you can jam on the rigging and get er done..
Regarding the plastic intake stuff, the flywheel cover missing would not necessarily mean water in the throttle body. That piece covers exactly what you said. The piece in the very front that clamps over the throttle body and serves as the front mount for the flywheel cover is the one of concern.(Nobody would need to remove it to remove the motor so it is probably a moot point) BUT With it missing and the motors stored upright the throttle body becomes a funnel.. Still, with the flywheel cover removed the air compressor has its air intake exposed that could allow water to enter there. It faces straight up and actually pulls air from the front (where the air filter is) through the flywheel cover and into the compressor. The more I think about it, I think I would walk away briskly.
Too many motors for sale, as you know.