CPU fan on full spin after dual drive SSD installation

I installed an OWC SSD drive a secondary drive on my iMac 27" mid 2010 (2.93, i7, Mavericks 1.9.3) following the ifixit guide and the OWC video. On my model there was an extra unused SATA port on the logic board. I left the original Western Digital HD in place. When I put everything back together I forgot to push the RAM back in properly and got a black screen and one loud beep every 5 secs. I clicked the RAM firmly in restarted and then I heard the CPU fan spin it's little socks off.

iStat reported that the ODD and HDD fans were running at around 1000rpm. The CPU fan, contrary to the audible whirring, was reportedly spinning at 0rpm. Yet iStat is able to confirm the temperature for all the heat sensors, including the CPU's.

An Apple Hardware Test returned the 4MOT/1/40000002:CPU-0 error. Great, so I must have damaged the LCD temp. connector.

I removed the LCD and triple checked the LCD, HDD, Ambient, Skin temperature connectors. They all looked good. I didn't remount the LCD screen, but connected my external monitor and turned on the iMac – open heart surgery.

On start up both ODD and CPU fans run at full blast. As soon as the OS is loaded the ODD fan spins down to an acceptable 1000rpm. The CPU instead continues spinning at full throttle. I've tried resetting the SMC and PRAM a number of times.

With the mac open I started testing. I created a small shorting wire for the LCD temp connector and tested it, no difference. Shorted the HDD temp connector, nothing. I tried switching round the LCD temp connector pins, nothing.

While working on it I'd turn off the maddening CPU fan by physically disconnecting the CPU FAN connector which sits on the logic board to the right of the CPU fan.

I removed the extra SSD thinking that maybe the system needed an extra mysterious SATA 2 port heat sensor. But still the CPU fan ran like crazy. And I've also tried flipping the (4 pin, 2 cables) thermal sensor connector next to the PCB on the original HD so that the darker wire is facing out. Still nothing.

I then went the software route.

– HDD Fan in demo mode only made the ODD fan spin faster - buggy and rubbish. Restarting was the only way to revert it.

– SSD Fan Control was equally useless, obviously. It doesn't offer an option to override the CPU fan's settings.

– smcFanControl seems to have no effect. I've tried creating custom fan spinning settings with it, but it doesn't alter any of the fans' spin speeds. I've also tried various flavours of the command /applications/smcfancontrol.app/Contents/resources/smc -k F2Mx -w 12c0. But still it doesn't override the CPU fan speed.

Lastly, I've only just noticed that the original HD SATA data cable was attached to the vertical port on the logic board, not the horizontal one as depicted in the installation guides. I may try inverting these.

What else can I try?

UPDATE: I've switched the two SATA data port cables (HDD vertical with SSD horizontal) on the logic board. Now the HDD is in the horizontal port and the SSD on the vertical one. It's made no difference.

UPDATE: I'm seriously considering hacking a resistor in place, as documented here.