Answering your questions in order, yes the most direct way of connecting to the mixer will be via the combo jack connectors. Bear in mind though, that your instruments don't necessarily output a true line-level so you may find the input levels to be lownin some cases. The best way to connect instruments such as keyboards and synths is via DI boxes and then into the mic inputs.
1: Yes you can use the digital patching function of your mixer to reassign input 13 to channel 1 and so on.
2: Currently stereo linking on SL Series 3 only works from odd to even numbered channels so you'd have to skip a channel and connect to 15/16. Then you can stereo link 15-16 and they work as stereo. It will take up two channels and two faders but younonly need to control one of them.
You'll definitely need to connect to the two separate inputs though. No Y-cables for this.
3: As I mentioned, DI boxes are the correct way to make these coneections anyway so you can use DI's to connect to inputs 1-12 that are mic-only.
Hope that helps.