Hi fitcher, that's a lot of questions in one posting! I'll answer as many as I can. First the reset switch is not essential, and Windows has a fairly similar function in Turn Off - Restart, so you can simply ignore those pins on the motherboard. Secondly it's not uncommon for one half of a connector function to be 3-pin and the other 2-pin. If the cable connector is 2-pin and the motherboard 3-pin, you can very carefully cut the housing between the 2 pins to make 2 single pin connectors. If the cable connector is 3-pin and the motherboard 2-pin, then you can cut usually depress the barb on one connector, push the connector out of the housing, insert it into the centre position and finally cut away the now unused part of the housing.
The switches don't mind which way round you connect them, neither does the case speaker. The LED's won't work if they are the wrong way round, but no damage will be done. For the first boot-up I generally only connect the power switch, then connect the other front panel devices when all is working. If the computer still won't boot, try resetting the BIOS. If that still doesn't work, remove everything from the motherboard except the power switch, processor with heatsink and power supply. If it then boots, add the case speaker, and see if you get a POST beep. Then try again with memory, then with graphics card and continue until you have a working system.