I have done a few 4.0l OHV heads and I have always torqued down the heads completely before installing the intake, never had a problem with mine or others.
Yes use that black silicone at the 4 corners and then across from head to head at each end.
No, you don't have to go up the head
Put intake gasket on at that time, on top of the silicone, then install the intake and torque it down.
If you feel more comfortable doing it per Ford specs then do so, it certainly won't hurt anything or change anything as far as silicone placement.
There was an issue of the intake bolts loosening up over time, I think that is why this step was added, I haven't run into that issue before but I haven't worked on every years 4.0l
Just scrape of any old gasket material off the gasket surface areas, you don't need to clean inside the manifolds.
Hot tanking is probably the only way to clean them in any case.
Yes, use the exhaust manifold gaskets.
You can use anti-seize but it won't help, lol.
Exhaust bolts just expand and contract so much they get stuck over time
Nuts on the studs are flanged and oblong so they can't back off
You should use grade 8 replacement bolts on the manifold