The AC at BTR has been broken for quite some time now. In fact, they just got a new compressor put in but the whole system still isn't working right, and so now they have to have someone come in and break something down to get at the problem(s). Hopefully it'll be working once that's all taken care of.
Thunder River has 8/9 boats technically available for use, however there's usually a few parked in the reservoir due to lack of daily need. The 9th boat I've heard they can't get on until both wave makers get fixed, which is still in the works.
The Boss just got its third train back from the shop last weekend, so not everyone on the crew was certified for three-train operation immediately. They worked very hard to get as many people certified for three trains as quickly as possible, including many of those who are not part of Boss's home crew but are just cross-trained at it. Three-train operation is only used on an as-needed basis; three trains do not start the day on the track (unless high park attendance is expected), so whenever the line gets long enough to warrant a third train, the ride has to be shut down until maintenance can transfer the train onto the circuit. In situations where they need to keep three trains on the track in case the ride gets very busy, but the line isn't long enough to warrant actually loading all three trains at that time, one train (typically the yellow train when all three are on) will be leaded (those bags are actually filled with 40 lbs of lead) so it will make it through the whole circuit without any trouble, and so it's easily able to made operational when it actually is needed.