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Why I am having phase difference between original and reconstructed signal in this simulink model?How can i remove it?

As @MBaz mentioned, you have a zero-order-hold block that introduces a delay + a sample time block that can introduce a delay depending on its settings. Not sure about the Encoder and Decoder block, ...
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Adjusting pulse amplitude against fixed noise variance to achieve a given Eb/No

The energy of noise in your $L$-length frame is simply $L\cdot \sigma^2$. The energy of your pulse is $n\cdot \lvert A\rvert^2$. The SNR over the whole frame hence is $\frac nL \frac{\lvert A\rvert^2}{...
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