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How to run this big data program in shorter time?

I need Urgent help. Actually, I can run this program when I used data 100 amplitude and 100 frequency but my data around 1000 amplitude and 1000 frequency. When I used more then 200 data its not run. Even if I used 200 data its run but take whole day. Please help me how can I used my whole data and get results in short time. I attached my Mathematica file. I am waiting for your replay. Please suggest.

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