I'll start by saying I'm new here so I'm sure I have a lot to learn, but do you really need to pull the motor to change the mounts? I would think not??
More to your question, even though I've never pulled a motor from this body type, I have pulled a fair number of motors over the years. For the most part I imagine it'd be like any other car or truck.
So You should have several of options. You can get or make a lift plate to use in place of the intake. This gives a nice center of balance, but can be a bit more cost and time. (I'm not sure I'd mount to an aluminum lower intake half personally, although that would probably work)
or I believe there are factory lift points on the front of the drivers side head and the rear of the passenger side. I 'think' I recall seeing someplace that ford even makes a bracket? or you could fab one.
or you can use 2 bolts in the head accessory holes running the chain or strap from on one side front to the other side back with the intake on.
or you can use 4 bolts into accessory bolt holes at various places on the heads agin with the intake on.
other thoughts; use good chain or strapping, and good bolts & washers. If you use chain be sure to protect your valve covers or anything else that it may hit or bump to prevent scratching.
also a decent load leveler can be a help if you have the extra lift reach, but you can also do it fine without one. In fact the cheep ones can bind up and work against you.
I would be to first check into changing the mounts without pulling the motor however.
If you do need to pull it, Just take your time. I've never dropped or damaged a motor puling it. Most times with two fastening points. Oh yea and watch for pinch points while your working.