Also, the fans actually plug into a hot-swappable container and that container plugs into the motherboard. So does the proprietary cabling issue still come into play?
I had a Google and couldn't come up with much info on this or useful pictures. Could you perhaps give some more details of what fans are connected and where/how they plug in?
Replacing fans with standard computer fans won't give you anything like the airflow as silent fans are far far lower output. It might be worth getting hold of a standard computer fan and swapping in place just to see if the system boots OK or not?