After some sleep, I think I'm able to take another stab at this. See the attached arcgis-dataspace.xml file (just change the extension from TXT to XML and view with Notepad++), which is an example file that you can use/modify after backing up your original if you wish. I think to manually register the enterprise geodatabase manually as I suggested earlier, you would need to create an "enterpriseDatabases" item entry as seen in my example file. I've also included a "fileShares" item entry as well for a folder called C:\data\content so that you can see what a registered folder looks like too. Using the info you provided, I substituted your parameters in place of mine to show what the enterprise geodatabase item entry should look like. The only issue would be the password, which AGS encrypts automatically upon successful registration. I'm not entirely sure how you might get past that issue, since neither of us will really know what your encrypted password would look like. I've made it all zeros for now. You could try adding this item entry to your file, then restarting the Windows service for AGS, then going back into ArcCatalog and re-saving your password in the SDE connection file properties, and re-validating your already-registered data store by clicking the Validate button under the Data Store section of Server Properties. That might work as it could re-set the encrypted password to the correct value for your environment. I'm not sure if this will work, but it's possibly worth a shot. If it doesn't validate, click the Edit Registered Database button and modify your connection information from there. Then click OK and try validating again.
As a last suggestion to register your data store using the ArcGIS Desktop tools, I would say to create a TNSNAMES.ora file entry for your database named m12yd223 and then specify m12yd223 as the only value in the Instance field afterwards. If the issue truly is the length of your host name or the inclusion of periods in the string, this may be a good work around.
