The "user1" ROM is equivalent to the BIOS in your PC - it does just enough to load a program off of the harddisk into RAM and transfer control to it. No game code or data exists in that ROM. KI doesn't have an operating system, it just loads the game itself and runs. Some later Midway game...
Some of the DK sound is synthesized in software by the 8035 and output to a DAC. Some of it's generated by purpose-built analog circuitry that the 8035 triggers. The only thing that's a sample in the ROMs is the gorilla roar, and that's stored in some bespoke compression format. You should look at s...
What language did you use for the business software? I can attempt to feel out explaining your questions from there better I think :) There's plenty you can do without even starting coding though when it comes to emulating a specific PC. You'll want to try and find the manuals for at least the chips...