Bitstream autocorrelation? - comparing two bitstreams - BER?
In order to measure BER, you need to compare the received data stream to a reference data stream that has the same data and is correctly time-aligned with it. Using a PN generator at each end tells you what the data is, but nothing about the time alignment.

In that case, you can use cross-correlation to find the most likely time alignment. With the PN9 sequence, this means trying every one of the 511 possible alignments in order to find the one that has the largest number of bits that match. Then, the number of mismatched bits in that alignment gives you the BER.

Is this the sort of hint you're looking for? If not, you need to make your question much more specific.