As I went through each field manually, with Binary Ninj. As I was checking the offset of the current byte, at 0x07, Wikipedia says: It is often set to 0 regardless of the target platform. I’ve changed it to 0x00. (Note: I think this field was probably ok as it is)
At offset 0x12, the value Specifies target instruction set architecture and is currently invalid. From googling, I found an article titled: Novell's Next Generation OS Will Natively Support Intel's Future IA-64 Architecture so I set the value to 0x3E.
At offset 0x20 we have the e_phoff which Points to the start of the program header table. It usually follows the file header immediately, making the offset 0x34 or 0x40 for 32- and 64-bit ELF executables, respectively. The value de ad be ef is clearly invalid. I replaced the value with 40 00 00 00.
At this moment I thought I fixed the binary and ran it, it ran and it gave me an invalid flag.