So with a bit of swapping you could change the fans and make it more quiet, I've done it with many older dells. For the front panel if you get a multimeter you can chase down the traces and find the outputs and solder on headers that will work for your current motherboard. Lastly for the SAS card, I have flash many over the years and have never had one fail. Just take your time and read threw the documents on how to flash and let it roll.
Good luck and keep us up to date with what you end up doing