Now knowing where my noise is from I have located the actual flex point
It seems it is from the aluminium frame rail where it seats onto the roof. I can roll back the roof and grip the rail and by flexing, induce the noise I have been suffering for couple of years. I tightened any screws I could find but didnt make any difference. By inserting a flat blade knife between the two areas I can eliminate the flexing .The blade acting as a shim.
So I have inserted some strips of plastic electrical tie at strategic points to shim up the rail. Took the car for a run and the creaking noise has reduced by 70%. Added a couple of more 'shims' and the noise is almost GONE!!!!!
How long it will fix the problem I dont know but at least I know where to look.
Hope this may help anyone else.:woot:

Hey there, has your bush mechanical fix cured the problem? I have a TJ that is now driving me nuts!

Hi
No it hasn't. It reduced the noise initially but its back and as bad as before.
I tried squirting some silicone between the rail and the roof but no better
Got so bad I gave the car to my wife. She never notices any squeaks or rattles.

theres a guy in syd that knows this problem and fix, he rebuilds sunroof, makes screws bigger and bores out holes, makes custom brackets/rails (more heavy duty) and replaces sunroof seal, bores out drain holes bigger and puts bigger silicone hoses to allow a steady stream of water to pass through without overfilling, takes out roof lining to and puts back in to do job properly, he was asking $2000 for the fix and leave the car with him 2-3days, he guaranteed lifetime warranty on all parts and labor to never fail, squeak, creak, vibrate etc...

too damn much to spend on such a minimal issue

Thanks for the replies... I was never notified of them, hence delay :)