I think that what they are referring to with the motor is perhaps the lack of mass air for the crate motors. It only half makes sense though, considering 87 and 88 cars were SD as well. If you decide to run one of those crate motors, you will most certainly need to swap from speed density to mass air. None of the cams (save the E-cam under certain circumstances) are SD friendly.
Otherwise, those crate motors are a drop in fit. There are only subtle differences in the engine bay. None of which, are things that you would notice during an engine swap.
Side note: If you decide to convert to mass air, I've discovered that it's best to convert your SD harness rather than swap in a 16 year old+ mass air harness from another car. PARTICULARLY if your SD harness is in good shape. Strange things happen to old electrical harnesses when yo uremove them from one car and bend, twist, and pull them into another. The other option is buy a brand new harness from someone like Ford Fuel Injection. Just thought I'd toss that out there.