You aren't going to get very far in emulating that game well. The most you can do is use either Glide64 or Rice's Daedalus 5.2.0, which comes with 1964 and also emulates the game RELATIVELY good, but with several still-persisting gfx issues. Those plugins are your best hope for emulating a game like this.
There are also sound (RSP) issues. You need the Project64 Audio Fix Edition to fix this.
http://www.emutalk.net/attachments/apollo/11017-hydrothunder-audio-audiofix3.zip?d=1060193261
Do not choose an RSP plugin for this game. Leave it set to none in this hacked version of PJ64 emulator.