Mk3 Ford Focus 2.0, No start, Alternator replaced, Relay continuously clicking

2011 Mk3 Ford Focus Estate 2.0 Diesel, Manual gearbox. 138,000 miles. UK

I live in the UK and have always done my own servicing and maintanence, but modern vehicle electrics I find more daunting. I am now retired.
I joined this site a couple of weeks ago while search for information to help me fix my car, which I have owned for 12 months. I have started to study the massive amount of information in here but would appreciate some help as to how to further diagnose the problem I have with my car.

Recently for a couple of days I found the battery discharging and had to recharge it.

The following day on start up the engine was running very rough, and on setting off down the road had severe loss of power. Message on the dashboard said "Engine Malfunction - Service Now" also lots of lights on the dashboard, Engine warning light, Glow plug Indicator etc. Just managed to get back home and stopped the engine. Tried to restart, but engine would not restart.

Suspected the Alternator to be at fault, so, after disconnecting, tested the diodes with my multimeter on diode setting, and got a reading both ways.

Replaced the Alternator with a new one. Also while partly dismantled, replaced the Timing Belt, Water Pump and Pulleys, and the Fuel Filter. Only to find the engine still would not start with the same symptoms as above.

On further investigation, I found with the ignition switched on, Relay 3 in the engine bay fuse box was continually switching at a regular frequency of about once a second, and also the Throttle Position Sensor motor was also energising at the same frequency. On trying to start the engine the starter motor would also engage in very short bursts at the same frequency. With the ignition off, if a door was opened and closed, Relay 3 would again start switching, and then stop after 10 seconds or so.

With the Starter Motor Relay bypassed the engine turned over normally. I swapped the starter motor relay with another identical one in the fuse box, and also swapped Relay 3 with another identiclal one, but this made no difference. Have checked all the fuses and also the ones in the BCM.

Have tried to start the engine on several occassions, and on one occassion the engine did turn over normally, but not start. (maybe due to air in the fuel line after filter change). But then on trying again back to the same symptoms.

Using Forscan on my Laptop and connected with OBDLinkEX Model EX101 2.2. Forscan said OBD need an update which Forscan could carry out, so update installed.
I have the following DTC: PCM P0606:00-27, P060C:48-23
PDM B12DC:54-2F, B12DD:54-2F,
DDM B12DC:54-2F B12DD:54-2F
HVAC U0422:00-2F
IPC U0400:64-2F

I would be very grateful for some help with the next steps to take with the above fault. I feel that the clicking relay is a big clue, but unsure how to proceed.

P06XX codes are, usually, internal module errors. 

P0606
 


P060C
 


Make sure that you have good powers and grounds at the PCM.

Thanks Chad
Investigating the PCM today