Has anyone had a similar setup/situation and gotten banned or had success?
I'm a lightweight when it comes to botting, but I figured I'd contribute my $0.02 to the thread.
I have a main account with 3 90s which I primarily use for tradeskilling. I'll occasionally xmog hunt or faction grind with Tyrael, and sometimes I run GB2 with my own profiles. I sold quite a bit of gold recently to pick up a few 2 month game time cards, so I reopened one of my other accounts (that was supposed to be my bot account) and have been running Kicks to get the toon up to speed. Note, the second account is apparently RAF'd (I forgot until I got the mount notification a couple days ago) and I have taken it through a few dungeons and raids with my main just for achievements. I only have one HB license atm, so the second account was pretty much on autofollow and not really doing anything.
Keep in mind that there's nothing in Blizz's terms about multiboxing being "illegal" or against the ToS. As long as they get their money, they really don't care how many accounts you have. Many people multibox to bring along pack mules for raids and whatnot. I don't think having two accounts on separate B.nets is an issue, either, as mine are set up that way as well.
From what I've seen in ban reports, it's when you're running 5-man RAFs through instances while AFK for 10 hours straight that you tip the Big Bad Blizz off that something might be up. All it takes is a GM to watch you for a few minutes for the ban hammer to come down.
This is purely my opinion, but I think you should be fine. If I were you and I wanted to do instance runs with my RAF account, I'd use one healer and something inconspicuous like a ranged DPS with the Singular profile. Definitely no tanks. I respect your aim to do everything legitimately, but it's going to get old and annoying very quickly (especially while trying to "maintain" two accounts at the same time).
If you wanted to play it even "safer" (for lack of a better term, I guess), make your RAF toon the healer and run HB on that account, then play your main legitimately.