board compatibility issue

Hi, i am working on a project where i need to program a controller for an internal combustion engine. Right now i am using an arduino mega2560 board along with a software called labVIEW for serial communication. I need to change some variables while the code is running, for that i am using labVIEW i.e. i change the values in labVIEW and it is sent to the board serially. Now i need to process some signals to trigger the generation of another signal for that i am using two signals as interrupts. The matter of concern is it is happening at a high speed like i want to go up to 6000 rpm or around that value. If signals come once in every 27 us, would the arduino Due be able to do this processing and serial comm together because with mega it is skipping the generation of that signal once in around 8 cycles, well without the serial comm too it is skipping?