Knowing that your fans only idle at 3600 or something low like that seems to make me thing something is wrong especially since my stock fans idle at 5400. Also, you mention that chipset temp is at 90 degrees where mine is 79 degrees with replaced lower airflow fans. I would certainly work on flashing the BMC. I have flashed mine a couple of times but these BMC controllers are crap. I moved my server from one location to another and one of the BMCs stopped working. I am going to flash again but something doesn't seem to add up with your temp and fan speed. Knowing these things are just north of junk, makes me feel like I will be flashing the BMC every so often.
. Other than the BMC being buggy, everything else is good so the server is still worth the money.