Can't help you on the first one because my electrical instalation runs acessible in its entire length. I've used some self sticking rubber channel (readily available in DIY stores). That's how it should be on any boat, in my opinion. It's a bit of an aesthetics problem but its a lot safer in case anything goes wrong.
Anyway, to the other two questions:
2) Soldered and shrink tube insulated. This way they sholud be smooth enough to slide in easily;
3) Trash the internodes and replace them with individual wire runs. Once again, safety and reliability gets improoved. The more nodes you have the more nodes there are to transform themselves in problem in the future.
By the way, funny you placed this post today beacuse I´m just finishing replacing the wiring on my Piver Nugget 24 trimaran. Another piece of advice is to make a hinged switch board, that you can acess easily either from the cockpit or from the cabin. Here's mine, almost finished:
Hope to have been of any help.
Regards from Portugal