Although I don't know the program, I should be able to help you find the file, but I also need your input to help with this, with a file name (the name you saved the file as) you can search for it, knowing the format it was saved in will also help as the link above gives the default save locations, so your file "should be" in one of those folders or your My Doc's.
You can't copy and paste the program into the new system, it would have to be a fresh install, which you will need to do anyway as that's what you have created it with, unless you were looking to use a different program ?
I did just have a thought, have you tried to launch the program from the problem system drive ?
To do this navigate into the Programs folder on that drive (NOT the new systems drive), go into the folder that contains the program you have been using, then double click on the specific program to launch it.
I honestly don't know if this will work, but it can't hurt to try, and if it does work you should be able to access your file the way you always have done, so if this does work, open your file as normal in the program, then select to Save As,,, then when the box comes up, select to save it to your desktop of the new system, then install the program (shutting down the other one first) on the new system, which will automatically associate the files types, and you will be able to use you file the way you have done in the past.
I would suggest not installing the program again until you have tried this, see if it will run from the other drive first, I know it's a long shot, but if it works it will be the easiest way for you to do it, also make sure there are no other files you want while you are in there, and repeat until you have all you need, but in future you need to adopt a safeguard to avoid this in the future, for ease of finding I suggest creating a folder in your My Doc's then select to Save As… and navigate to that folder, that way you know where the files are.
I also strongly suggest creating backup's of the important files (anything you need to keep safe), and the more important the data is, the more often you back it up, when a system goes bad you can lose everything in the worst case, so keeping backup's on a separate external drive, and\or disks\thumb drives is a must, worst case you still have the data as it was from the last backup, so you would only lose the data since the last back up, anyway see if this helps, if not I will dig deeper to see what I can find.