i have no idea about MoS2 and the substrate but for metallic catalysis you can use ethanol or acetone with ultrasonic bath before process and vacuum pump with argon-hydrogen to clean the substrate
I think, Aqua regia ( a mixture of hydrochloric acid (HCl) and nitric acid (HNO3) at a ratio of either 3:1 or 4:1) cleaning is working for your problem. Refer more and use it to clean substrate.
You can clean the SiO2/Si substrate with acetone + isopropanol + Ethanol + DI water and sonicate it 15 min for each. Finally vacuum dried the substrate.