"a" or "an" before abbreviation

The CMoS and APA style rule is to choose the indefinite article based on how the abbreviation is pronounced.

"An MS" is correct.

You have it right that a different article goes before. It does depend on if you pronounce each letter separately (initialism; "an MS Society walkathon") or pronounce it as a word (acronym; "a MADD after-school event"). In these examples, the first takes an an and the second takes an a.

For your examples, I think you can do it either way because I do hear people prononce it as MS as often as I hear them pronounce it as manuscript. I'm somewhat of a purist, and I usually spell out "manuscript" instead of abbreviate it as MS. On a forum, it's not going to matter much, but of course in a query or an actual manuscript you would want to spell it out anyway.

Technically, "MS" is not an acronym, but an intitialization. Acronyms are things that transform themselves into things resembling actual words, because they can be prounounced (NASA, DACA, FEMA, etc.). Some of these even manage to morph themselves into actual dictionary words (snafu, laser, radar, etc.).

caw

I agree with Anna Iguana, at least as far as how I've always been taught. It should be written the way it would be spoken. I would say "an MS" and "an R&R".

I'm no grammarian by any stretch of the imagination, but the way I see it is that "a" or "an" is defined by the first abbreviated letter. All vowels used as the first letter of an acronym will be preceded by an "an".
Some consonants begin with a consonant sound, so they will be preceded by an "a", but some consonants begin with a vowel sound instead. Those are the ones that may cause confusion. I'll show you what I mean below.

F = ef (This is the first consonant of the alphabet which, when used as the first letter of an acronym - ie. FCC - would call for the use of "an" because it begins with a vowel sound.)
H = heych, eych (Depending on your regional usage, this will be either "a" or "an".)
L, M, N = el, em, en (Same rule as F.)
R = ar (Begins with an a sound, therefore same rule as the e-sounding F, L, M and N.)
S, X = es, ex (Same as F, L, M and N.)

I hope that helps.