Editorial woes

While I've perused these boards in the past, this is the first time I've actually made a post. Thus, I'm not entirely certain if a lengthy, multi-question post like this is appropriate, but I hope that it's acceptable.

I recently agreed to edit scripts for a group -- specifically, English scripts translated from Japanese, intended to be used as subtitles. While I have some confidence in my English, I've never used it for anything but casual, informal conversation or formal essays, and a quick look through the CMoS didn't help much. I apologize in advance if I get some of the terminology wrong, as it's been a while since I dealt with it.

Stutter -- how should i go about expressing this? Do you only capitalize the first letter in the sentence -- provided that the word in question is the first one in said sentence -- or iterations as well? Should you use a regular hyphen to separate the parts or some kind of dash? What is a breaking point?

"W-What do you mean?"
"W-what do you mean?"
"Wh-What do you mean?"
"Wh-what do you mean?"

Long pauses -- while these are usually set off using ellipses, I find myself wondering if an em dash wouldn't be more appropriate (though even if that's the case, I doubt I could do much about the prevalent ellipses culture). Note, these are not sentences that are cut off abruptly; they are merely left to hang until they are resumed. The reason why these are broken up in the first place is timing; in essence, if there's a significant pause, the subtitles will drop from view, since no one really wants to have them hanging there if there's no actual dialogue. Imagine a pause of some four to five seconds between these:

"Have you ever experienced..."
"...doubts?"

Em dash vs. en dash -- when you use a dash to set off a parenthetic thought -- like this -- would it be better to use an em dash or an en dash with spaces around? In academic writing I'd never hesitate to use the em dash, but those who are unaccustomed to academic texts often find it ostentatious or even obnoxious. Since dashes are rare in subttiles, I haven't been able to make an accurate assessment of the current trend. Note, I tend to emulate dashes with hyphens on forums, so this is not an exact representation:

"My sworn brothers-Adam, John, and Dan-will aid us in our quest."
"My sworn brothers -- Adam, John, and Dan -- will aid us in our quest."

Disjunct adverbs -- specifically, short adverbs or adverbial phrases at the end of beginning of a sentence. I've always used commas to set these off (with a few exceptions), but I'm curious as to what would be considered acceptable?

"I've been wondering about that, too."
"I've been wondering about that too."
"I've never seen him myself, though."
"I've never seen him myself though."
"Would you consider my proposal, then?"
"Would you consider my proposal then?"

Comma splices -- are these acceptable, provided that you, as as editor, know what you are doing? While I abhor comma splices in general, there are some that are perfectly acceptable, and some that I find questionable. While some manuals state that comma splices are fine if the clauses are short -- especially if they are similar in nature, and the subject is the same -- I still hesistate to use constructions like these:

"Don't worry, he'll be all right."
"Don't worry; he'll be all right." (I'd prefer a semicolon or a period)

"It's all right, he'll recover in no time."
"It's all right; he'll recover in no time." (I'd prefer a semicolon or a period)

"It's not a car, it's a bus." (This one I find ludicrous, to be honest, since there are so many ways to rewrite this)
-- "It's a bus, not a car."
-- "It's not a car, but a bus." (It's been a long day and I'm tired, but I think this would work, too)

That ended up being quite a lengthy inaugural post, so while there are a few other things I'm wondering about, I'll leave it like this for now. Thank you for your time.

Edit: Ah, the parsing rendered that unreadable. I hope this works better.