looking at doing a Gen3 swap ???

First, there are lots of answers in the existing threads. Take a look around.

1.which is better - personal preference. Cost. Etc. You'll have to ask Modern Muscle about tuning for a 6.4 in an old car - not sure where that sits.
2. Car or truck front cover, either one works. Car front cover with accessories is a cleaner look. That's the only real difference. There are a few bolt holes different on the blocks, but not a big deal.
3. They are the same
4. They are the same
5. intake depends on front cover you use
6. ?
7. ?
8. ?
9. long discussion below

Rebuild - the factory service manual (available online on lxforums, links given in other threads, some by me, do a quick search)

There are really only a few different short blocks and heads offered for hemi motors since they came out in 2003.

03-08 5.7 motor - earlier ones did not have VVT, later ones had VVT. Can run them without it.
03-08 5.7 heads - good head, lowest cfm in stock form.
6.1 short block - no VVT. Good motor. Out of production.
6.1 heads - higher flowing than 03-08 heads. Hollow valves from factory.
09-current 5.7 short block - Ask someone else - I don't know.
09-current 5.7 heads - named 'Eagle' heads. Similar intake port to 6.1 heads, and similar flow to 6.1 heads with smaller chambers.
6.4 short block - Ask someone else - I don't know.
6.4 heads - called Apache's - highest flow numbers, port cross section is pretty big.

Eagle intake - plastic, has long and short runners
Apache intake - plastic, has long and short runners
03-08 5.7 intake - plastic, has long runners only, smaller intake hole than 6.1/eagle
6.1 intake - aluminum - has long runners only

You can look around for performance figures from the different combinations.

That should get you started.