I noticed this is an older post, but I had a similar issue with squeaky door sealings on my car. I tried various sprays, but nothing worked long-term. Eventually, I replaced the door sealings with genuine parts from a dealership, and it made a big difference.
For the bonnet foam padding, I had that problem too. It helps with noise and vibrations, so replacing it can be worthwhile. I found new padding through Mantaline – they offer custom elastomeric applications that might be just what you need. It was a good fix for me and really quieted things down.