So far, I have found a scene modifier, and even decided to check out the original NES version for myself since the code seems to have been mostly directly taken from the original, minus pointerse. So far, the comparison reveals that the scene itself was chopped and the credits are not in a separate scene, so I'm hunting down the individual musical hits to see what's going on. A code comparison helps me in this fashion, too, considering the NES's processor is simply a step backwards from the SNES. 
I have discovered the Ninja Gaiden staff roll theme exists in Ninja Gaiden Trilogy. To access, simply use the PAR code 81804318. All I had to do was compare and contrast to the original NES version. The key difference between this one and the one that is used is that this one is non-looping and ends after about a minute and a half.
Considering I have been doing comparisons (especially musically), I have determined that the unknown jingle that was found is also from the original Ninja Gaiden, and it is unused in the SNES version. Its corresponding NES version (at least the US version: I haven't checked the Japanese version yet) also appears to not use it to my knowledge, as any values that have been dummied out in the SNES version either play nothing or play SFX. I am hot on the staff roll's tail at the moment... now all I need to do is see if the cutscene data still exists. If so, I'll hack my way into the staff roll, probably via a pointer modifier.
...and via my secret music hunt, the results are in. The good news is that I was able to restore the staff roll for the original Ninja Gaiden with the SNES version. The bad news is that the cutscene code had to be implanted from the NES version because it got deleted... literally. Thankfully there's enough room for me to just simply copy the bytes. And with a little bit of code hacking to ensure that the ending plays, the staff roll is back up and running.
These come from the US version for both the NES and SNES versions. First, go to 2A604 in the SNES ROM (this is based off of a hex editor... 04 17 FF should be the three bytes preceding it). This is exactly where the staff roll would have gone. Now, go to 125CB in the NES ROM. Copy 21E (or 542) bytes and overwrite those bytes in the SNES ROM starting at 2A604.
Now, in the SNES ROM, replace all hits for AD 00 03 preceding where you implanted the cutscene code with A9 0B EA. If done correctly, when you start the game, you'll instantly get the ending with the staff roll.
Here is the result via YouTube. |