Hello,
At this point, you're easiest bet is just trial and error, as none of the usual references state what length bolt goes where. Doesn't look like those bolts hold anything but the waterpump, so where the long bolts bottom out the short bolts go, and where the short bolts don't thread the long bolts go.
Good luck!
Here is a cool picture of H20 pump and bolt layout
http://wumopis.com/dodge-pump-truck-water/
Copy and paste the above link on Google search... Yes, It's the same as yours!
RepairPal Certified shops can diagnose and repair your 2001 Dodge Ram 1500. They provide transparent pricing with a minimum 12-month or 12,000-mile warranty on repairs and services.