Can Tiruvaradhanam be performed with two Salagrama-s? (That is, by placing each Salagrama in two separate boxes and performing all the Asana-s and performing snAsanam for both individually). Can Tiruvaradhanam be performed without Sanskrit shloka-s but only with appropriate Azhvar and Desika Prabandham during the respective Asana-s? Can tirtham from either sarvArtha thOya or arghya vattil be used for grinding sandal wood paste?

It is specified that one must not have two Salagrama-s. If one has two Salagrama-s, as mentioned in the question both the Salagrama-s can be placed in individual boxes and Tiruvaradhanam performed individually. Until one has 4 Salagrama-s, one must follow this practice and one must make efforts to obtain two more Salagrama-s.
One can seek one’s Acharyan and he gives his consent, one can certainly do so. Ask your samashrayanam Acharyan and he will teach you. After obtaining his permission, proceed to do so.
One can use the tirtham from sarvArtha thOyam for grinding sandalwood paste. Instead, one can use the tirtham from Tirukkaveri.