It's sounding like it is cheaper to do an engine transplant than refurbish bearings in existing engine?
No doubt there could be a number of reasons for your engines issue. 
Does the knock go away soon after engine is warm or is it there all the time? Wonder if your 3rd cylinder is giving you a hint that the following recall is relevant and soon to be a bigger issue; is your VIN captured in this recall and if so was the recall a new engine or a modification to the existing engine? The same article also talks of faulty injector hitting piston...cam carriers cracking.
DEFENDER2.NET - View topic - TDCi Reliability and Longevity
Anyone know about the following service bulletin - was it mandatory to all 2007 TDcis? 
 
Land Rover Service Bulletin SSM38792, 2.4 Puma Engine Knock Noise.  
Title: 2.4 Puma Engine Knock Noise.  
Type: LD - Defender - All Years - Special Service Messages - Engine  
Name / Part No: SSM38792  
Info Type: Service Bulletins  
Version No: 1  
Date Uploaded: 21 Jul 2008  
Models: LD - Defender  
Title: 2.4 Puma Engine Knock Noise.  
Last Modified: 21-JUL-2008 09:44  
Category: Engine  
Symptom: 497000 Engine Noise  
 
Content Issue: Heavy audible knocking heard on start up.  
Cause: On start up oil pressures can cause the piston cooling jets,  (PCJ), to latch into a zero flow condition. Due to hysteresis effect in  design the jets do not unlatch until the engine is warm and the oil  pressures lower again. During this time with no pressurized oil jet flow  to the lower pistons / cylinder bores, overheat and scuff conditions /  damage can occur.  
 
Action: Replace the engine assy but ensure only engines post serial # ELD00080707063602 are used.  
This condition will not occur on vehicles post assured Vin# 9A767162.  
Engines post the info above are fitted with modified PCJ internal springs and this issue is now closed.
And here:
Just a moment...
The early 2.4's (2007-2009) had known engine failures due to some oil  channel valve that became blocked causing a knocking noise and later  failure.
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