Stat loop? Do you mean the room stat link at the terminal strip?
Do not link the CH pipes? You mean cap them off. I would link them in case there is flow for any reason and the pump is then moving water.
If the diverter motor has been removed there will never be any flow.
Removing the diverter motor. Would the maker back up the warrantee?
Many combis are cheaper than system boilers for the equiv output. Can the diverter motor be removed and the 3-way valve set at the CH only position. Would the makers go along with that?
Many diverter valves need the pin depressed to set then in the CH mode. Thats easiest by setting the motor in CH and removing the connections.