Er1 and Er2 are signs that the gauge is not receiving data from the ECU. They are not ECU trouble codes. The wiring job probably deleted some wires that the gauge requires to function.
Without a proper connection to the ECU, the gauge will not be able to get trouble code data, so theres no way to tell if the ECU really is having problems (which is probably isnt if its running).
You can run a 04-06 R1 without the gauge cluster, but I would get a service manual, and see if you can get into Diagnostic Mode from the gauge cluster. If you can (which I doubt you will be able to), you can check each function out one by one to be sure you are getting the correct info from the sensors.
If you cant get into diag mode, I would check the wiring schematic in the service manual and confirm that all wires leading from the ECU to the gauges are there, and hooked up right. You can get the service manual in PDF form online. Try r1-forum.com. Im sure there are links to it there.
Why do you think it is in Safe mode? I dont believe there is a safe mode on that year R1. It either lets it start/run, or it doesnt. That being said, according to the service manual, Er-1 and Er-2 should result in a UNABLE to start/run condition, which makes me think the gauge is really not communicating with the ECU!