I think FreddyNerk gas you the best possible answers based on the information you have provided so far. Modern diesel engine electronic control modules has multiple ways of control engine speed and load. They also over time change defaults. While some ECM's come "bare" with no programming, most others have a "basic" program that will allow an engine to start and come to idle or minimum rated speed.
How was the new MDEC module "damaged"? Engine ECM's are usually pretty darn robust devices, they don't usually just fail, they get killed, mainly due to issue on the power supply and/or grounding. Early on many were damaged by improper welding procedures on the engine skids of the package/truck/machine they were installed in.
As you been told before,
Not coming up to rated speed is most likely a configuration issue if you are using the same device to provide the speed bias input signal. As I remember (and someone like Freddy or someone else with direct MTU experience may know better) is that the MDEC used a 0-5 VDC (actually .4-4.5VDC) default speed bias input, but newer ones I'm told can be configured to use many different analog speed bias input signals, such as 1-5VDC, +/- 3VDC, 500 Hz PWM or 4-20mA to name the most common I see. Speed control over CAN is also becoming more popular, but since you said the old CAN wires were not connected before, then speed bias over CAN was not likely how it worked before. What is the speed bias output signal out of your Deif AGC? I think this has already been explained to you above.
On the CAN error, again, likely a configuration issue or a change in the basic ECM programming looking for an active CAN signal. CAN errors of this type are either the CAN signal is out of range or the ECM is polling for a device on the CAN network and not getting a response. The troubleshooting guide for your specific engine and control should help you properly diagnosing the faults.
Engine service tool softwares are usually only provided to authorized service providers, since stricter emissions regulations this has gotten to be more the case. MTU may offer a customer version of the software, but you likely have to go thru an MTU dealer to get setup (typical of most all engine manufacturers). Most third party softwares I'm familiar with only allow reading codes, resetting certain alarms and changing a very limited number of parameters.
At this point I really think you need to contact your servicing dealer or ask the factory for help directly. Independent service providers may have technicians or field engineers how have the experience or technical expertise, but may not have access to the proper software or factory technical support.
MikeL.
