I believe the Clymer manual says that on some bikes there is enough room so you do not have to remove it from the frame but I would recommend taking the entire engine out of the frame since I prefer to have a bit more room. I am a TOTAL n00b when it comes to this and I have not re-assembled my bike yet but getting the engine out of the frame wasn't very difficult and it allowed me to work more easily on the entire engine.

Before ya start pullin bolts, KNOW exactly how many there are and be sure ya dont overlook one.
Take a piece of cardboard and draw the head cover and put a slot where every bolt belongs, and stick them in, along with their sealing washers on those that have them,
That will avoid a real puzzle on reassembly,, Much time and frustration saved.
There is one in the middle that wont come out, be sure to put it back in before ya start reassembly.
There is one on a corner that is upside down,, make sure to solve that before ya build a bear trap goin together.
The Correct sealant and the right way to apply it is very important, There are threads on such.
Dont leave that scrunched up lump of what looks like a pot scrubber out. NO reason to pull it,, anyway.
Pay attention to the figure 8 O-ring,, Cant let gasket goo get in there.
If ya somehow get rid of the oil in the head,, add a bit,, doesnt hafta be runnin over or makin a mess..
And before ya start torquing the bolts, unless youre an experienced mechanic,, lets have a little time on How to do it without causing a problem,,

If ya have a way to lift it ya can set it on a cinder block and use the same wooden shims from Lowes they use shimming door frames to make it rock solid. I have a come along hangin in the shop and use 1/2 inch woven nylon, Woven,, because I think its stronger than wound,, Might not be now,, because they use polyester for a filler, but the bike is 380ish pounds and the harness is four going down,,

Havin the bike off the floor just that little bit is helpful, havin it straight up and down is great. Just leave the support hooked up, with out being tight enough to lighten it on the block and shims,,

Gonna hafta find a replacement for my Old Woven nylon rope that has no polyester in it,, Its noticeably heavier in the hand,, but nobody sells it anymore,,

And NO,, my way is not OSHA approved and if ya decide to go with it,, Youre doing it without me tellin you its smart.
Your call,,
That said, Ive had mine off the ground about five times,, But only with the old style rope. I did use the new rope to pull the mower out when it sunk after a rain,, Doubling it up and makin sure its not across anything sharp,, mehh,, prolly be okay,,
Be sure to run whatever ya use between wires and cables and the frame, dont crush anything,,
And hopefully you can tie a Bowline..

AND
Before ya decide where the gasket goo goes,, look at the head cover and the head,, if the head has a spot that looks like goo goes on it, but the cover doesnt,, then dont..