The package lm-sensors might be what you are looking for.
And as you suggested fancontrol.
Be sure that all the fans that you are trying to control via software have the 4 pin connector.
"A PWM capable fan is usally connected to a 4-pin connector (pinout: Ground, +12V, sense, control)."source
When I run
pwmconfig which is a part of fancontrol I get
/usr/sbin/pwmconfig: There are no pwm-capable sensor modules installed
It will guide you if you have compatible hardware.
Here are some scripts to use in conjunction with that generated config file.
I assume that you could set a higher value here.
label fan1 "Side Fan"
set fan1_min 1000
label fan2 "PSU Fan"
set fan2_min 1000
label fan5 "CPU Fan"
set fan5_min 1000
But as I said, I can't test this myself, since my hardware don't support it, I can control my fans from the bios, but it's a grade of 3. I use it for keeping my fan's slow and silent.