Receiving shifted 8 bit data with cyclone v custom phy transceiver ip.

You can find some example on alterawiki.com. The first example is for Custom PHY. That does't use manual mode but sync state machine mode, but it would be still helpful.

http://www.alterawiki.com/wiki/cyclone_v_transceiver_phy_basic_design_examples

If you don't use an encoder, such as 8B10B, it is difficult to find word boundary automatically (in manual/sync state machine mode) because there is no special bit stream which can be used as a word alignment pattern. In general, K28.5 code is used as a word alignment patter if 8B10B encoding is used.