Ryo Suzuki for some model like Ine-san you have SD model in the HumansAFS and a ( HD ) model in the NPC folder ( for cinematics with more polygons ). My Friend you are NUTS ^^ to want to put the head of Yu Suzuki on the face of Ine-san
But for your question for changing characters in Shenmue it's really easy.
We'll take two caracters of the disc 4 of Shenmue 2 for exemple ( Xiuying Caracter ID = SYE and Shenhua Caracter ID = SIN )
Extract the HumansAFS in a folder. Now take your hex editor and open the PKF and PKS file of Xiuying as you know it's SYE.PKS and SYE.PKF now replace all the caracter ID of Xiuying ( SYE ) by Shenhua's Caracter ID ( SIN ) like screenhot here:
You must do that for PKS and PKF and don't forget to save ^^.
Now you must make the reverse that mean than you must replace the Caracter ID of ( Shenhua ) SIN.PKF and SIN.PKS by Xiuying's Caracter ID ( SYE ) with your hex editor and save, it's obligatory. Now rebuilt the HumansAFS.
Tha last step it's the Human.IDX, you must reverse the Caracter ID like the screen:
and the result here:
In fact the Dreamcast believe that Xiuying is Shenhua and reverse, with this technique we can replace the caracter but sometimes there is bugs and this does not work but the technique is exactly the same for Shenmue 1 and Shenmue 2, the only difference is that in Shenmue 1 all the caracter ID include 4 letters and for Shenmue 2 it's 3 letters, if you have problem Ryo let me know.