The Blue Sky will be good with whatever else you do, and accurately control the solar part of the charging. If the other parts are also doing as well, the solar will not interfere with anything else.
For the alternator cutoff switch, I really like the Blue Sea full manual one. Draws no parasitic and comes with a very nice switch setup. They also make a manual/auto one that is very similar, if you want to have both ways of control. Here is the thread on putting ours in. To use it properly, it is best if you can see a battery monitor, either on the solar or shore charger, or stand alone, so you know when to shut it off or turn it on, based on amps to the batteries.
http://www.classbforum.com/forums/f8...rade-3586.html
A replacement charger for the Tripplite is a bit tougher, depending on what you need out of it, and if you are willing to do some manual work with it or not.
First off is what do you need. If you don't need an inverter big enough to run the microwave or other high load, you can get the smallest of the Magnum chargers, which are actually not as spendy as you might expect, especially if you are OK with modified sine wave. You do need to add an ARC50 remote and BMK monitor kit to them to get the accurate charging methods, though. The disclaimer is that there is a glitch in their programming that makes it so the unit does not do a full charge cycle (when it is in the desired return amp mode) unless the batteries are somewhat discharged and showing lowered voltage. This is a problem if the solar, or surface charge, is holding the voltage up on low batteries, preventing a full charge off of the shore power. In those cases you would need to manually start the charge cycle when you plug in--a 5 second job off the remote, but you have to remember to do it. Once into charge cycle, nothing more is needed and it will fill the batteries completely and not poorly interact with the solar.
I haven't found any chargers that do better than that, especially for the price of the smaller Magnums. Magnum has stated the glitch will be addressed in the next rev of the remote.
You can get equally good results from a Progressive Dynamics charger, but you would need to manually watch the amps going to the battery on a battery monitor, and switch it to float at the right time, and maybe put it back into bulk several times. Doable but inconvenient for sure.
The system described, and almost exactly what we are putting in, won't complicate things much at all. You would have an added shunt at the batteries, the different separator, a couple of remotes. The charger would still be a inverter/charger combo like the Tripplite. The solar would be essentially a standalone addon.
We have done the bench testing of most of ours already, and will be doing the final install this winter. Ours is more complicated mostly due to the 4 GC2 six volt batteries going into where the generator was.
We found that when we had the Tripplite, it would get our two GC2 Trojan wet cells only to about 85% full, and couldn't be tricked into doing another charge cycle to finish them, so you probably are getting similar. If so, you certainly could gain some capacity by getting all the way full.