Stuart Scuba has multiple boats. They typically have a boat operating in Stuart as well, but doesn't go out as often. I dove with them once out of Stuart and it was pretty amazing, the amount of sea life seen on descent was unbelievable. Vis was horrible though and we dove a site where an old bridge was dumped. Tons of lionfish. I actually took a hit from a LF on the dive. It wasn't drift diving.
Jupiter is awesome. You can dive Stuart Scuba, my personal favorite Kayalami (guess we can't call it Sl8r anymore?), JDC, Scuba Works, and many others. I believe Scuba Works goes out around 8am. This is all drift diving. I've not experienced any op requiring a buddy. Most put guides in the water and they prefer you follow the guide if they aren't familiar with you. I think this fact is what makes divers feel more welcome on one charter over another, at least for me since I'll dive the one where I'm not treated like a new diver.
As for BHB, we average 1.5 to 2 hours on our dive times on an AL80 (many times with plenty of air to spare). 2 hour dives are absolutely awesome. I honestly don't even notice the depth during the dive and just enjoy looking for critters. The dives don't feel that long, so you know you're having a good time. If you've never dove the site, hit up the BHB Trolls forum and see if someone will let you join them. There are a lot of guides as well. We grudgingly let other join us. 50% of the time they have some equipment failure and end the dive within the first minute, 40% of the time they aren't good divers causing silt and end up running out of air early, and on rare occasions they are a pleasure to dive with. Knowing this, we don't babysit. If you run out of air early, surface and swim back, it's a very short swim. If you have an equipment issue at the beginning, stand up and walk out, it's that easy. Solo diving? No one cares, locals do it all the time. You'll get the most out of the site if you dive with someone who knows their way around.