Thank you for all the kind responses. Like I stated in the Downloads Request Thread, I used the Internet Archive to look at captures of the BCFiles main page from 2011-2015. On pages that loaded correctly (ie showed files from around that date and not the error page that only showed stuff from March 2011 and earlier) I was able to click on the links in the "Latest Files" section. If the actual page was captured (and not the stupid error page), I was able to copy the file name of the mod and search for it at the gamefront online backup. Unfortunately for some files, only the error page was archived, so I can't search for the file name. I'm sure its in the gamefront archive, but without the filename, I can't search for it. If I try to search for the mod using its Title (ie the name the author gave the mod above its file name), the search will turn up squat 95% of the time. Because of this some stuff (SFRD/SFSY's Chimera Shuttles, Nostromo, Runabout, Bajoran Prototype, and the Subspace Amplifier from Enterprise, as well as Phoenix's Marco Polo Class) can't be retrieved cause I don't know their exact filenames. I've tried guessing them with no luck. Also it seems the Terran version of the Joan of Arc is not on the gamefront archive, because I inputted the proper filename but got no search results for it.
I focused mostly on the SFRD/SFSY, GMunoz, and Phoenix's stuff because they seemed the most affected by the server bug. But there's other stuff and I encourage all of you to take a look at bridgecommander.filefront.com on the internet archive and maybe try to grab some files when you have the time. As for me, I'm pretty close to the space limit Dropbox gives to free accounts, so I probably won't upload anymore files unless I'm sure it can't be found anywhere else.