Hi I have a Lenovo T440 BIOS that I am trying to find a clean BIOS image for. I ran the gjuj39us.exe installer and it decompressed its contents to C:\DRIVERS\FLASH\gjuj39us\GJETA3WW. Inside this folder there are two files: $01DF000.FL1 and $01DF000.FL2. The FL1 file is only 9MB while the FL2 file is 193KB, not 16MB like the backup rom I pulled directly off the chip. How do I get the other 7MB to make the complete 16MB rom? I have tried opening the backup BIOS and update BIOS files and comparing the HEX differences, but there are too many differences to form a clean new image from. I just want a BIOS image that is just how it was from the factory.

T440 or T440P - I'm not sure if same, and you didn't link BIOS download page, so here we are
Generally speaking, the FL1 is only BIOS region + some other stuff you wont use, so you can never get complete BIOS image from that. You will need to rebuild from your dump (which has FD, ME, GbE region + BIOS region), or use another full dump to rebuild from etc.
You will not be able to get anything "like it was from the factory" you will have to build a BIOS image, and transfer your board specific details (Serials, UUID, LAN MAC ID etc) into it, then you can program back on.
During that process I would also advise you go ahead and update/clean the ME FW while you are at it, in case ME FW is messed up.