Regarding your problem, I suggest you to remove with a spatula or a knife all the residues of the stucco work, also intervening on that stucco that shows signs of decay or even is about to jump, or at least shows cracks, trying to remove it as much as possible.
Then you should go to a tile adhesive retailer and buy a product such as Mapesil Ac by Mapei, which is a pure silicone/acetic sealant resistant to mould for movements of up to 25%. It is available in 30 shades, which combine with the pre-existing coloured joints.
It appears like silicone cartridges, it is a specific and not too expensive product. With this product, you will solve your problem.