Your comments

Hope your hand is ok!
Hi Frederick,
For the problem with the VREF on the MC3 not showing on the MD4, the VREF error may not have been seen as a popup on the MD4 if it was present at boot-up, if you were using 3.15 or earlier. This was solved in IQANdesign version 3.16
24023 MD4 do not show errors from other master modules on startup
Could happen if another master module sends out error messages before the MD4 GUI is up and running. Fixed.

For the isseue with the MC31 block diagram mapping, it would have made sense if you downloaded, then rearranged the block diagram and started measuring without sending. This because measuring works based on channel ID:s, and they don't change when rearranging. But it sounds as if this was not the case here.
When you had the issue on version 3.15, I assume this was not a beta but the relesed version 3.15.16?

Glad you like the MD4 routing function!
There should be, but there seeems to have been a problem with all the 3D models not showing up on for the last couple of days
That sounds really strange. When you had the input mapping problem, are you sure you did not relocate the inputs in the block diagram and started measuring without first sending the updated application to the MC31? 

Yes, a VREF error on the MC31 should show up as a popup on the IQAN-MDx, if you have a master display in the system and they are connected on the Diagnostics bus. You should also be able to see this error if measuring in IQANrun or IQANdesign.
The error description of the DOUT sounds as if this DOUT has been damaged, except for the part where you say that it seems to be an issue with the I/O mapping.
What do you have connected on DOUT-J?

For the problem with the VREF, does that error continue to shwo if you disconnect connector C2? Most cases of VREF errors are due to the VREF being overloaded or shorted.
There currently seems to be a problem with sending larger updates via the G2 modem. Online diagnostics is also affected. 
We are checking if there is a problem on the Proemion server side.
If the IQAN-MD3 is not involved in any calculations for the application, and is only used to show values from the MC2 in on the display pages and in the measure groups, tune adjustable values and view the log, then it is enough to just connect the IQAN-MD3 and IQAN-MC2 on the Diagnostics bus, like this: 

You don't need to set any J1939 source address on the modules. The only thing you need to do for addressing is to make sure that exactly one of the IQAN master modules is has IQAN address 0. (note this is not the J1939 source address)

On the IQAN-MD3 display pages, all channels from the IQAN-MC2 automatically becomes available, like this: