Yes, you can plug it into a fan header, but now I'm wondering if after you cleaned the CPU off, did you give the rubbing alcohol time to dissipate, or did you immediately apply the thermal compound. Also, try to enter the bios and see if you can get a reading on the aio pump rpm (I know that the fan rpm doesn't exactly translate to pump rpm, but it should indicate how much voltage if any at all is being given to the pump).
Also, while I've never had an AIO water cooling unit (Only custom hardline watercooled :/) when you start the system, put your hand on the block and see if it vibrates at all.
To be honest this is really beginning to sound like a pump issue, but there still is the likely hood the there's not enough contact pressure between the block and the cpu, or that there's something in the way interfering with thermal paste.