Interesting you ask this as I`ve just completed the exact same thing. Due to the constraints of doing it in my garage with not a lot of height clearance - taking the whole engine and gearbox assembly out was out of the question, not to mention it`s a lot harder/fiddly to take the whole assembly out than just taking the engine out. Seeing as though you only need to work on the engine, then that`s all I`d take out. Even though the manual (probably) doesn`t say to remove the hood, you`ll find things a lot easier if you do remove it.
Apart from all the other ancilliaries that will be covered in your manual - there are only a handful of bolts securing the engine to gearbox so it`s a pretty straightforward job. Just whack a jack under the box when you remove the engine, and don`t forget that of course the slant will want to tilt as soon as you lift it (depending on how you`ve attached the lifting chains) - this also applies to when you reinstall the engine, it`s going to want to tilt to the side when it rests on the engine mounts, so you have to kind of guess the position that it will 'fall' to (if you know what I mean).
So all in all, I believe it`s much easier to remove just the engine if that`s all you need to do. Having said all that - the engine swap that should have taken me a weekend ended up being 3 weeks because of all the little problems that come with swapping engines
