Can you suggest me a reliable method to store the data as the experiment may last for 9 hours with sampling frequency around 100 kHz?
Are you sure it's possible at such rate? If you do the math, 100 KHz is 100000 times per second, and there are 6 outputs, so 100000 * 6 = 600000 times per second. UART (serial) packets require at least 11 bits to transmit 8 bits (a byte) of data (aka payload); thus 600000 * 11 = 6600000 times/bits per second (66 Mbps).
Of course, this is assuming 8-bit outputs; if those require more than one byte, then you have to even multiply 66 Mbps by the number of bytes per output.
As you can see, in theory, is not possible at 100 KHz; for that, you may have to use a MCU clocked at least to 100 MHz, and a faster communication like UDP over "Fast-Ethernet" (or better) wired LAN.
I was simply copying the data from the serial monitor to excel, but later I found that serial monitor is erasing values after a certain time. I have also tried with the PLX-DAQ, but it is crashing after 2-3 minutes.
I think the data volume is too large to process it in realtime. Maybe you should dump the binary data stream first, then do the rest.
Serial buffers usually aren't that big, so you need to dump the data into a file as soon as is received. At least I know
RealTerm can do binary dumps from a serial port, but I'm not sure if there would be an issue with file sizes.
Keep in mind that if you somehow managed to transfer 6 bytes 100 000 times per second, dumping a 9-hour session of a continuous raw data stream, would result in a file as large as 18.1 GB, yikes! :o Definitely don't save that in a FAT32 drive!