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 Infact queing delay is variable, and three RTTs are not enough to measure a good estimate of queing delay. In this case, we need to measure the analysis of like arround 10-100 RTTs to get a sufficient good estimate of queing delay. The more RTTs we have in a set for a router, the more better estimate we can fetch.
 Once we have the queing delay from source to router A, we can easily find the tramission delay. Once we have transmission delay we can figure out the Incoming data rate of that router.
We know that RTT from A to R1 = 2(PdA + Td1 + Qd1), lets consider Pd, is 0 compare to Td and Qd  then
RTT from A to R1 = 2(Td1 + Qd1)
Td1 = RTT/2 - Qd1
RTT from A to R2 = 2(Td1 + Qd1) + 2(Td2 + Qd2)
                          = 2(Td1 + Td2 + Qd1 + Qd2)
Td2 = RTT/2 -Td1 - Qd1 - Qd2

In order to get a good estimate of TD we calculate the average RTT for each hop avgRTT1 = avg(RTT1, RTT2, RTT3) for router R1.
Hence the transmission delay for nth hop is given below:

In order to find queue occupancy, we need to know the incoming and outgoing link datarate.
Queue Occupancy (Qo)= incoming rate - outgoing rate
Now the incoming rate of R1 is Td1 and outgoing rate of R1 is Td2. So,
Qo1 = Td1 - Td2
Qo2 = Td2 - Td3

I am still working on figuring out the estimate of buffer size at each router, using the above calculated metrics.