Post a link of the flap rods you refer to. I bought some for my A8 V8 petrol and they were one piece milled aluminium.
These ones although for a petrol I think are available for diesels:
https://www.gruvenparts.com/audi-vw-...-linkage-arms/
I would check for operation first, I think they are either connected or not. Mine were snapped and need replacing hence me buying new ones.
What's the reason to clean the inter-cooler? is it very dirty or has lots of oil residue in it?
My advice to clean and fix or improve what you have before thinking about spending big on brand new manifolds. Just make sure everything functions as they are meant to.