Is it permissible for a person suffering from obsessive doubts (al-waswasa), who has long-standing uncertainties about the purity of certain things, to deem them pure, and would this be considered an attempt to convince oneself for the sake of comfort?

There is no cure for obsessive whispers (waswas) except to disregard them and pay them no mind. If you doubt the purity of something, the default is that it is pure. Do not rule it to be impure unless you have certainty upon which you can swear an oath. Ignore the whispers and act upon the default; this will remove the whispers.