I have determined why your conversion went so poorly. SNESMod only goes up to 64 instruments, and your instrument numbers are so scattered (and all past 64) that it's no wonder why the conversion was not even remotely successful, even going beyond 99 (I used my 2012 build to correct that, because my 2008 build was unable to move instruments past the 99 mark)!

Here's a successful, but slightly glitched conversion due to loop points needing optimizations: https://app.box.com/s/ftaviy9v90zcvdzmnkh1nt7zxnuqi7sj

...and the source IT file: https://app.box.com/s/y0w8ldzv2zz1o1yoogzpio1cwwh83uzg

That explains it!
I had a giant list of instruments I was using in Renoise, and when I removed the unused instruments, it didn't collapse them all down to the bottom slots.
Thank you KFF for solving this mystery! I'll have to remember this in the future...