the SC clunk will be an unrelated item. the clunk just means that the supercharger is old and all the clutch material is worn off. while the clutch is elctro magnetic the material won't affect the operation but it was there to dampen the impact when the magnet activated. now the metal clutch is just touching the metal pulley when it engages so it makes a clunk. 

Is there any way of repairing this to reduce the clunk?

i have heard of people pulling the clutches appart and putting a damper between them. what type of material you would use i am not sure something that has good grip but won't stop the magnetics. maybe a rubber pad?

Ok to update this, other than the voltage issues I can't fix and don't understand as its the same on 2 looms with and without the computer plugged in, the issue is now isolated to a hesitation below 3000RPM. Normal driving RPM between 2000-3000RPM (possibly lower but hard to test conclusively), the engine just seems to load up but really struggles to accelerate,  then as the revs increase the engine noticeably surges and hesitates as it passes 2,500 and 2,700RPM with a great surge of power at 3000 and away we go. The engine itself sounds like its really struggling, heavy labouring and the exhaust sounds really deep and drony. The throttle also becomes very touchy around 2500-3000rpm (harsh on and off), clutch slip has also become very difficult at running temp, the engine needs at least 1200RPM to slip the clutch smoothly, any less and the engine shudders quite heavily. When under light throttle it's not as noticeable but I think that's more of a perception and load than the severity of the fault (as the clutch slip issue would indicate)
 
The issue is, this has now just come back. I had managed to sort this out somehow, the car drove perfectly for about 20 min, pulled from 1500RPM like a SCed engine should, power delivery was smooth and consistent with a constant increase in torque then hard pull from 3000. I turned the engine off, checked a loose wiring on the battery for a temporary boost gauge, started up and the problem was apparent as soon as I started to drive (couldn't clutch slip).
 
I'm planning on replacing the leads however I've inspected them all and they're all around 8kOhm (might be leaking though), I've checked the coil and its within limits the plugs, cap and rotor are brand new (less than 50km since the engine was first started). Replaced the AFM with a spare which looked in better condition, replaced all vac lines (except the front line to booster), new fuel filter, checked timing again, added temporary earth straps. TPS couldn't be adjusted better, ICV is functioning.
 
I've noticed when running the timing light on the primary lead it misses every now and then and the revs, timing and sound alter fractionally but it doesn't sound as if the engine has a big miss or anything sinister, if it wasn't for the light it would be almost imperceivable. Trying to work out if this is a dead coil, ignitor or maybe just an earth or lead leak (or normal)? I haven't noticed it on the No1 lead but it might be a chance thing. 
 
Anything in there that I could have missed to cause this hesitation issue? 
 
Cheers,
 
Nick

You describe a very similar problem that I have, I find mine to also feel as if something is restricted, either air/fuel up until it hits around 2800-3000 RPM, then it feels as if that restriction is lifted and the car surges on. I've lived with it for a while now and havent been able to find a solution so I'm keen to see if you find one.

I've read of someone who replaced his cooler with a front mount (corolla) and it solved his issue but other than my top mount being stuffed (leaking) I doubt changing it would have a great affect. I'm still not convinced I don't have an air leak somewhere but it's going to involve replacing/checking the whole intake tract which I don't have time for at the moment. It's the only thing I can think of other than ignition which would cause it to be apparent at low rpm but fine higher in the revs.

Unfortunately for me it makes the car undrivable and especially so when I'm used to a 200kw v6 which pulls from 1500rpm.

Mine is a long way from being undrivable, its my daily. It certainly is noticeable though, sometimes more so than others. It can bog down particularly badly going up a steep hill if I haven't put the foot down a bit before.
 
Have you got a boost guage at all? I do notice mine is still making plenty of boost under 3k, it just sometimes doesn't feel as if it's doing anything until it hits 3k... 

Yeah mine is between 8-9psi from 2500 rpm and its noticeable, if the boost is up around max it really drones like its really struggling. 

I thing you should try new ig leads next. Even if it isn't them it would be good to replace the old ones anyway.