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.

Yes we have tuning now for the 6.4L as well as engine management systems