Neither of those sound good.
My Duo has a creaky seat pan. The rubber surround definitely contributes to creaking noises and particularly in the back seat.
The seat pan is pretty easy to pull out and should give you clear access to all the control circuits.
When do you get the clunking noise? Stick movement? Rudder movement? Just randomly?
How tight is the fit of your wing on the lift pins? With the wings on and pinned, is there any fore-aft or up/down play on the lift pins?
Have you checked the resonant frequency of the wing during annual inspections? You should find the original resonant frequency of the wing in the paperwork from the factory. I'm trying to remember what it is on our Discus A. I want to say around 120 cycles/min, but don't quote me on that. It's been several months since we did the annual. If you've never done this, it's pretty simple. Rig the glider, move it off the dolly and with the wings level, stand at a wingtip and start bouncing the wing up and down until you find it's natural frequency. Then time it for 30 seconds while counting the cycles. Double that number and compare to what the glider originally had. A major structural flaw should change that value pretty significantly. A few cycles/min aren't anything to be concerned about.
Those are at least points I would start with.
A little bit of play can be resolved with the use of very thin shims on the lift pins.
Where are you located? It would definitely be worth the piece of mind to have a good mechanic look at it. Load up the wings, listen for odd noises.
We sadly lost a pilot locally that had questions about the assembly of his glider. Please follow up on this. If something doesn't seem right, it probably isn't.
Morgan