1st time computer building/wiring question

Item 2 - you made a big error. The wires coming out of the PSU with 4-pin Molex connectors on them do NOT EVER connect to the mobo. The 4-pin Molex connectors are to provide power to IDE-type devices like HDD's, optical drives, etc. They also are used often to provide full power directly to fans, etc, but they can NOT control fan speeds - they only can run a fan at full speed unless the fan itself has some speed adjuster. On the same set of wires is another smaller type of 4-pin connector that is used to power a 3½" floppy drive if you have one - this connector is almost useless for anything else, and it certainly does NOT go anywhere on the mobo.

If you want to control case fan speeds by the mobo, the fans in question must be plugged into one of the mobo's SYS_FAN pinouts. NOTE that these are power OUTPUTS from the mobo. They are NOT inputs to the mobo from the PSU. That's how you blew the first mobo - by putting power from the Molex lines into the SYS_FAN port of the mobo.

Most mobos have two SYS_FAN pinouts. Sometimes only one of these is speed-controlled by the mobo, sometimes both. Each is designed for only one fan to be connected. BUT if you do some wire splicing, you CAN power up to TWO case fans from each SYS_FAN pinout. It is usually considered that each pinout can handle the heavy momentary start-up current for two fans, but not more. If you choose to do this, whether you are using 3-pin or 4-pin fans, check the fan wiring diagrams for wire color codes. Do NOT splice together the wires for the fan motor speed signals from the two fans - leave one of these wires not connected to anything. But do splice together the matched wires from each fan into one connector to plug into one SYS_FAN pinout. For example, IF you were working with 3-pin fans, you would connect both reds together near the connector on the end, both blacks together, and only one Yellow wire connected to the connector. Wiring color codes for 4-pin fans are different from this.

If you want all your fans to run full speed all the time, you can supply power to them from Molex 4-pin connectors direct from the PSU. You can get simple adapters that convert a 4-pin Molex to a 2-pin fan supply connector. In this case, there will be no speed signal fed to the mobo, so your mobo will never know what the fan speeds are. Molex outputs have a much higher amperage available than mobo SYS_FAN pinouts, so you can use adapters to connect several fans to one Molex output from the PSU.

So you understand, the mobo does control of the CPU cooling fan via the CPU_FAN pinout, and of the case fans via the SYS_FAN pinouts. Each of those pinouts is the power source for the fan. In the case of 3-pin fans, this is accomplished by varying the voltage supplied on the +VDC line (red wire to the fan) from 0 to 12 VDC max. In the case of 4-pin fans the system is a little different. The Ground and +12VDC lines are that way all the time, and the fourth line is a special PWM signal. Inside a 4-pin fan case is a small controller chip that uses the PWM signal to control the flow of current from the +12VDC line though the fan. BOTH types of fan also have a speed signal line on Pin #3 of the connector (Yellow wire for 3-pin fans). This signal is a series of pulses (2 per revolution) generated inside the fan motor and fed back to the mobo via this line so it can be monitored. It is not actually used for speed control - speed control is based on temperatures measured with dedicated sensors, and accomplished by varying either the voltage or the PWM signal. But the fan speed signal can be displayed for you. Also, for the CPU fan, some mobos check it as an extra precaution - if it fails (indicates no fan turning), that type of mobo will send out an alarm beep and shut down the system very quickly (not waiting for the CPU temp to rise too far) to protect the CPU from disastrous overheating with failed cooling. The mobo has several features to protect the CPU and ensure cooling, so it usually is wise to connect the CPU cooling fan to this mobo pinout and not directly to the PSU via a Molex connector.

Re: Item 1, I don't know why you cannot get it to work with the SSD plugged in. Certainly if you did that at the same time as having the Molex line connector plugged into the mobo SYS_FAN pinout, it would not work, but that has nothing to do with the SSD.

Your SSD is set up to connect to the mobo just like a SATA drive. This means it has two connectors for cables. One is wider - 15 pins - and you plug into that a power supply connector from the PSU designed for it and other SATA devices. The other is narrower - 7 pins - and you connect this by a small ribbon cable to one of your mobo SATA ports. Assuming you are using the SSD as your boot device, you probably want to connect it to the first SATA port of your mobo.