I have finally been able to get this working last night!
In response to Girish I have logged the call. They have sent me a java file that I had to replace as Girish suggested needs to happen. This however did not solve the problem. The new file did not work at all. I reverted back to the old and the support engineers then went ahead with troubleshooting. (My installation paths are not default or the versions are incorrect - we did not troubleshoot the reason for this, but I have found in other scripts that the different installation path wasn't working and have fixed the path in all scripts required.)
The actual solution:
SRM does not require the SSO database to be distributed according to the engineer.
Furthermore it seems as if v1 of SSO does not like it when the database is distributed when there are no changes. That was the reason it broke.
I therefore proceeded with the second SRM installation straight after the first. The last time I synced the SSO databases was after the VC installations.
I have my reservations with this solution, but have confirmed with the engineer that it is correct. I still need to test the system extensively.
The next version of SSO (v2) shipped with vSphere 5.5 apparently does not require manual database synchronization. It was also completely rebuilt and might be more stable than the current. I will wait for that version when I have the choice. The other option would be to not use linked mode and run two completely seperate SSO servers. It would still be v1 though unless you wait for VC 5.5.