Using the 555 is a pretty bad choice here.
Your first 555 would be easily replaced with a crystal oscillator, producing a more stable tone; for maximum efficiency and sensitivity, you should low pass filter, no matter how you produce a square or sawtooth wave, both the tone you transmit, and what your receiver picks up, so that you only get a harmonic signal at the fundamental frequency.
The comparator alone doesn't make too much sense? That looks like you half-understood a PLL or a correlator, but then didn't really do the integration.
Now, your system is supposed to measure times very accurately. The 555 is really not suitable at all here, as it's wildly inaccurate in timing. Time measurement is really the domain of crystal oscillators, and it would be much wiser to do it with a crystal oscillator.
So, I think, the honest answer here is: Drop both your 555. They do nothing for you that something else couldn't do just as well, but probably easier and more accurate.
Generally, I don't think your timing methodology makes too much sense; I'd recommend drawing your measurement procedure as finite state machine, and building exactly that from digital gates.
PS: There's a reason why microcontrollers are so popular in the last 40 years; making you do this project without one is not really worthy of a final year project, where you're supposed to show you're able to solve a real-world problem with real-world methods on your own.