It appears (from your description above) that you may have applied the foam before the silicone fully cured, and now the silicone is trapped between the wood & foam. The foam is an insulator, so it's designed to prevent air-flow (i.e. curing).
I don't know enough chemistry to know if there could have been a reaction between the uncured silicone and the foam, and part of what you're smelling could be formaldehyde from the foam.
If it were me, I would tear the foam out to allow the silicone to fully cure before re-applying the foam.
If the underlying silicone is still sticky, I would also remove as much of that as possible, allow any residue to cure, and start over.
If anyone has a better solution, or knows the chemistry for sure, please input.