The major problem won't be endian-ness (unless your unix machine uses a non-intel processor architecture) but merely the migration of 16-bit-code to 32-bit-code. The "processor" used on machines running DOS, the awful 8086, used to split memory in segments, each one being 64k in size and being nearly the same as the next one, merely shifted by 16 byte.
Thus the segmented address 0x1230:0x0010 is effectively the same address as 0x1231:0x000
or 0x122F:0x0020
Due to this fucked-up memory addressing scheme, 16-bit 8086 applications did some really strange stuff, which is difficult to port to machines having "straight" non-segmented memory access.