I have a cheap new CV that I bought off ebay for $40 to go in mine as it has been clicking for over 60K but it has not got worse.  I haven't put it in so I do not know what they are like.  
I have had both my front shafts out - I think they are the same length but I never measured them.
I had similar experiences with my 80 subaru - the quality of aftermarket repaired, reconditioned and new driveshafts varied - they all clicked when put in - some went worse and were returned and some went quiet once they were run in.
In all cases the quality of the boots was crap and never lasted as long as the CVs themselves - the suburu originals were very good though so I assume it would be the same with aftermarket vs original for freelander ones.
Because I never trusted the aftermarket boots I used to wrap the lot up in glad wrap.  If you wrap the CV and boot in glad wrap when on the car - not tight and stretched- give it a bit of room to move -  it worked really well - also works well when you have split a boot to stop crud getting in.  I held the wrap on with cable ties - on one the axle and one around the housing. Surprisingly the wrap lasted as long as a boot in some cases - but is easy to replace.  Wrap in the right direction so the wind does not try to unwravel it when the wheel turns.
So
"Questions (yes I am asking some of the seemingly dumb, but have a plan).
Are L/H and R/H driveshafts the same length?  Dunno but think so
Has anyone else had a similar problem?  Not on a Freelander but yes on a Subaru
Any variation in articulation spec between years?  Dunno - but doubt it
Is a Freelander driveshaft a Freelander driveshaft regardless of year and model?  Dunno but doubt it"
Has one of the new boots split already?  
Why not just put your old shaft back in with new boots and see what happens and keep your new second hand as the spare.  Will outer boots (designed for full articulation) fit on the inner?  If so - fit outer boots all around.
Sorry - I cannot be more helpful - but some other things to think about.
PS - I hope you are using new hub nuts are they are a one use only item - they have to be something like 320 whatevers in torque.
Good luck 
Garry
				
			 
			
		 
			
				
			
			
				REMLR 243
2007 Range Rover Sport TDV6
1977 FC 101 
1976 Jaguar XJ12C
1973 Haflinger AP700
1971 Jaguar V12 E-Type Series 3 Roadster
1957 Series 1 88"
1957 Series 1 88" Station Wagon
			
			
		 
	
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