I'm in the process of setting up something similar. For connections, there are a couple of different ways to go about it, but I decided to go with camlock quick disconnects. Take my advice and go with
BobbyM's products. I ordered about half mine before he came out with the new stuff, so the other half are from him, and are much easier (note, it looks like he's down for a few days catching up from the holiday rush, but if you aren't in a hurry, they're worth the wait).
For tubing, you'll need enough silicone to reach to your various implements. I'm planning on at most going from my BK to pump, pump to chiller, chiller back to BK, so I needed three sections of tubing. With the camlocks I can unhook the tubing and go between MT, BK, and HLT as well. For camlocks, I put elbow barbs and type B camlocks on all the hoses (BobbyM's elbow barbs for hoses are great), with the exception of the hose going into the input of the pump. On that hose, I went the BobbyM's "Big C" camlock with the wide hose barb on the end going to the pump (to hopefully cut down on priming problems), and elbow/type B on the other end of the hose.
For the rest of the connections, I've got type F camlocks screwed into ball valves on all my vessels. On the pump, I've got a center inlet so I've got an adaptor to cut down to 1/2" and then a type F without a ball valve. On the outlet, for the time being I've just got a ball valve to regulate flow and a type F camlock, and so far I haven't had any trouble with priming, but if I do I may have to change that around to get the air out.
The rest of your questions are really up to you. I'm upgrading my chilling (IC to CFC) since I've got the pump. I've got coolers for my MT and HLT, so I've already installed valves in them. For the time being I'm going to continue batch sparging, since all my vessels are on the same level, but may think about upgrading to fly if I decide to add a level so I can gravity transfer one vessel. A second pump would make fly sparging easier on a single level, but I'm not quite there yet.
Oh, I also stole
this idea and put my pump in a toolbox. I also got a
wireless remote for the pump power, and, of course, and
GFCI converter for plugging it in. Good luck!