I want to connect PJ64 and a GB ROM, but I don't have a plugin, or a clue, on how to do it . Any ideas?

Use the N-Rage Input plugin, and make it use the Transfer Pak. Note Transfer Pak emulation (in any plugin) is far from perfect, so don't expect flawless Pokemon transfers.

You will have to save in a Pokemon Center for it to transfer your Pokemon and would suggest backing up your save before using in case something happens to it during the transfer.