Normally, on those later trucks/engines, The OEM manufacturers choose to send the MPH signal, from the rear sensor on the rear of the tranny, up to those engine's ECM, THEN the engine's ECM would send a precalculated signal (say 30,000 pulses per mile) up to the OEM dash/speedometer.{note: now, all oem "dip switches, in back of speedometers could be set the same for all trucks, BECAUSE the engine's ECM made the calculations, for different axle ratios and tire size =that was a different number programmed in engine's ECM, too}


Note: This is cheaper, for the OEMs, because they only had to put one sensor, at rear of tranny, instead of two sensor(one for engine; another one for OEM speedometer) Two sensors were common, on older truck with earlier electronic engines.  


Your MPH problem is probably either the MPH sensor, at rear of tranny, or its connector, or its wiring, going up to the CAT ECM
(IF there is only one sensor, on this "converted truck"; which I assume to be the case) 
Note: Cruise switches go to CAT ECM, so if the CAT ECM had a good MPH signal, then your cruise would probably work, EVEN IF the OEM speedometer didn't work, Because the OEM speedometer is just an output from the CAT ECM(again, I am making an assumption, of how your truck is wired, but pretty sure it is new enough that this applies)  



Question: did you guys remove engine OR engine and tranny during that C-15 repair? If so, maybe something didn't get hook up, by the tranny, OR wires got pulled too hard, trying to remove engine and the connectors' wires got pulled out, OR wiring was left loose and the driveshaft/u-joint ripped it apart. 

Have you guys crawled under truck and looked around?