How do I use the ALTLVDS_RX megafunction with 12-bit

Yeah, essentially for link training, you first use the bitslip feature of the ALTLVDS_RX core to align the bits within a nibble - you can do this by comparing the nibbles as they come in to both halves of your 12bit training word. Once you get a match with one or other half of your training word, then you look at the whole word, and if you find that your it doesn't match, you add in a 1 clock cycle delay to the nibble stream to flip them around (this can be done with a mux and a register stage).