Hello zenseidk,
I'm going to be out of touch for a few weeks, but the Due is a good choice for your project with its much higher speed, memory and the ability for each pin to have its own interrupt.
Yes the Due is a 3.3V board which applies to all pins - be careful as it is more sensitive than 5V boards and cannot tolerate 5V signals. It would be good to post what power supply voltage the fuel sensors have and what the output signals look like ... a specification sheet would be helpful.
You will need to translate all input voltage levels to 3.3V and all 3.3V outputs to back original levels. There are many methods of doing this, each having its pros and cons. Luckily, you don't seem to have numerous signals to work with. Please search the forums for voltage level translation ... there's a good pdf somewhere but I don't have a link to it.
On the bench the logger works fine with a signal generator. The calculations are good, fairly constant and everybody is happy. But when I attached the 4 flow meters, the numbers that were logged were fluctuating wildly, even though I could read the output on the handheld display to be very stabil at 1060 L/h for the supply line and 900~500 L/h on the return line. The handheld display is fed data via RS485, so the frequency output is a separate output for use with some external data logging hard-/software.
I would be good to know frequency range and what the signals look like from the flow meters. Note that may need around 10K pull-up resistors as MPU's internal pull-ups are quite weak. If the outputs of the flow meters are open-collector, then using pull-ups to 3.3V will improve the signal and also do the voltage level translation.
I see in your sketch that you could comment out the pulse generator in the main loop as it is not being used ... this will gain some extra performance.