Yeah, milestone 1 and 2 are pretty simple but I have seen the case where students come in the lab and they don't even have the schematic and simulations ready. When that happens, they don't even finish milestone 1. That's why I told you do your schematics at home, simulation them and so when you get to the lab it's only to build.

With milestone 3 what you want to do is generate a random number (a random number generator circuit is provided in the lab manual, that one is 8 bits so you may want to reduce it to 4 bits) and compare that random number with a value generated by a four bit counter. The comparator can be four xnors ( one for each bit, if they are the same, it will give 1, if not it will give 0). The outpit for these four comparators (xnors) are inputted  into an and gate which will serve as the input signal to side you described. When the random number is equal to the counter value, a pulse will be send to activate the led or buzzer, which will at the same time activate the counter that checks reaction time(milestone 2). An external switch must be built to stop this counter. Remember  to stop a flipflop, without erasing it values you have to stop  the clock.

One issue you may have is that since your  random number generator is moving  and the counter is moving, they may not be synchronized to do the comparison. One possible solution to this is to store the value from the random number generator in four SR flip-flops, one four each bit. Put an external switch as a single clock input to those flip flops. When you switch it on for a small while, if each output of the random number generator is connected to an S input, and each R input is connected to ground, these SR flip flops would be in memory mode and so should store the values they receive from the random generator.

another option is to manually input the random number, just to test whether or not your circuit is doing the comparison and generating the pulse(stimulus ) to activate the reaction time counters .

I hope this helps.