Namaste Shubraji, Dilemma: As My Ishta devata is Narayan/Vishnu I use a tulsi mala for japa… but if I am also a Shankarite Advaitin from a Philosophical point of view shouldnt I be wearing Rudraksha instead?

Hari Om. It is advised to stick to the mala for japa according to your ishta devata. You can continue to follow and have faith in Sankara Advaita – the ishta is the form you use to reach the formless Infinite. It will be appropriate to use tulsi mala. There is no conflict. Adi Sankara established the panchaayatna puja (worhsip of 5 deities) – His connection with both Shiva & Vishnu, is documented in his biography.