Hi,
let's split the questions in sub-problems.
Problem 1: "If something goes wrong while running a program the same error is keep on repeating(even if i run some other program the old error is thrown) and i have to reinstall NS3 again to over come it. have reinstalled over 5 times :("
Perhaps it's useful if you tell us what "goes wrong". If you're accidentally deleting stuff, it's normal that you'll have to reinstall everything. However, usually this shouldn't happen.
We need to know the error you are facing, how you did install ns-3, the ns-3 version, etc.
Problem 2: how to implement the system described in the paper. Here are some bad news: it will be extremely hard. The amount of modification the paper authors did seems to be very high, and without a proper description, it's next to impossible to replicate everything exactly. Your best chances are to contact the paper authors and ask them if they can share the code. probably they'll not give you the code they are working with (i.e., the one with their latest modifications), but they could be keno share the code used for the paper.
If they don't, you'll have to study in detail the AODV implementation and try to understand what they did in each of the papers that the authors kindly provided as self citations. Be warned that this is not a simple task, as it involves a lot of reverse engineering and (often) to have to cope with the small bits that everyone forget to mention (and that often are very important).
About where to start *exactly*, study the tutorial and the internet module section in the manual, with a special attention to the routing models part. Then try to read the AODV module code (you'll need to have already a good knowledge of the AODV RFCs). While you're studying all this you'll become expert enough that you'll have no issues in creating the scenario, so don't worry about that, it will be easy compared to the rest.
Hope this helps,
T.