To set any file to run as administrator you need to go to the directory containing the file (N3V Games/TS12/bin), right click on it, select properties then the Compatibility Tab and there should be a tick box with run as administrator next to it, make sure this is ticked. This is for Windows 7 but I think it is the same or very similar for Windows 8. If I am wrong I am sure a Windows 8 user will correct me.
In your original post you say you installed another version, was this to the default directory or one you created especially for Trainz. Others who have had problems with Windows denying access have created a new directory for Trainz and told the setup program to install to this directory instead of the protected program file directory. It is probably still a good idea to run the Trainz executables as administrator but this can get round many problems. If you have a lot of downloaded content from the dls or third party sites it is possible to copy some of the directories from the old install to the new one so that you do not need to redownload the same assets again. They are mainly in the User Data directory but I cannot remember exactly which ones, however, there are a number of threads on the Forum that have the details.
If you do re-install make sure you run the setup file as administrator (right click the setup file and one of the options is to run as administrator) because I think this can also get round many problems with access since during the installation certain permissions are probably set for the game. I say this because many of my executable files in two separate installs of TS12 do not have the run as administrator box ticked but I have never had a problem running Trainz.