I'm still having problems with clonking over uneven surfaces I have replaced the anti roll bar bushes and drop links but the problem is still there.

I have noticed that at the top of the suspension strut there is a metal cup and a large rubber fitting that's attached to the body work. On the passenger side there is a gap between the cup and the rubber this is less on the drivers side.

Should the cup and the rubber be together? I have tried tightening the nut but can't move move it.

Ideas welcome

It sounds as though the top mount has gone. Can you post a photo?

They're easy enough to replace. Might be worth sending an email to our man in Lithuania:

[email protected]

As he seems pretty price competitive for this sort of stuff (1 Lt = about 25p)

http://manodalys.lt/product.php?id_product=1500750169

He's on this forum as well.

Not sure how to post a photo but it does look as though the top mounts may have gone the rubber around the cup is perished as well.
It looks as though to replace the mounts I will need to compress the springs it that right?

Yes.
You can remove the struts from the car without undoing the nut, if yours are anything like mine were (extremely tight top nut), you wont be able to do them in-situ.
Undo the three bolts securing the mount to the inner wing, and remove the two bolts holding the strut to the hub assembly.
You'll also need to remove the ARB link and unclip the brake hose and ABS cable.
Once the strut is out, you can put the compressors on and remove the top nut.

There is an Allen key socket in the top of the damper rod, but both mine just split when I tried to undo the nut (while holding the rod with an Allen key).
In the end, I managed to initially loosen the nut by clamping the top washer in the Vice, then once it was loosened, I held the damper rod with a pair of 'Mole' grips.
If you pull the bump-stop down and grip the rod right at the top it won't matter if the grips scratch/mark it.

I can thouroughly recommend Manodalys for the parts, his service and communication is fantastic, very, very helpful.
Manodalys experience

I've had another look and one of the mounts is almost new and the other although perished a bit seems ok.

The noise over uneven ground seems more like a rattle than a real thump even small ridges set it off. Potholes don't seem to cause it to happen.

If you jack up the side with the dodgy-looking rubber you should be able to see if there's any play in it.
Try and watch the rubber as you jack it, and jack it on the hub, not on the chassis.
Alternatively, jack the chassis until you have around 4" clearance under the tyre, then put a plank or long bar/pole under the tyre, and lift up on the tyre to lift the strut, you'll see if there's any real play in it.
Be careful not to lift too hard though, best to get an axle stand under the chassis as well.