Installing a Rainsoft Silver Series Timer Box

actually, the piston rod should move up and down, it might be tight but it should move.
I need a little more info in trying to understand what you mean by " timer". The timer mech is removed from the front of the case. When you talk about "bolting it down" are you referring to the 2 vertical screws holding the entire case to the valve body?
Start at the begining, you removed two small screws,holding the cover on the back? then one screw with a washer holding the piston rod to the case? then 2 vertical screws, holding the case to the valve body?

first of all, did they replace the timer motor? and fix the problem?
did you bypass the unit and remove the pressure in the tank(push down on the brine valve until the water stops flowing into the brine tank) , {but if your brine float valve is already shut off by the water height in the brine tank this won't work, if so then you have to remove the black brine line and push down on the brine valve until water stops squirting },

this could help in "freeing" the piston rod, allowing you to put it back together. notice that one side of the piston rod ,where it rides on the screw , is thicker than the other, it won't fit the wrong way,if it does something else is broken.... Hope this helps Joe