For 61388 you don't need the serial or the disk, it will probably try to download when you first start up TS12. However if it doesn't, you start Trainz proper, not Content manager, click "Get New Content", there are three tabs, Paid, Free and Upload, click Paid, ignore the large list and click the Redownload all purchases button and it should start downloading probably two or three concurrent downloads, you can cancel them if your connection won't stand it and repeat for each one, a bit tedious but it works I guess.
Doesn't matter where you originally bought it for Pre SP1 DLC so long as it was registered on-line with N3V. New DLC purchases don't even have to be registered now as you can only get them via in game digital download.
If you want to save DLC stuff thats been downloaded, it's all in the new Userdata/packages folder, just copy it somewhere, you can zip it up to save a bit of space. Then if you have to reinstall for any reason, you can just stick the packages folder back, run a QDR if TS12 doesn't do it anyway, and it all works, plus avoids downloading it all again.