OK, I just installed SNESKey on my 75 MHz notebook for a NES EMU, so I made a list of steps for you:
Step 1: Add SNESKey to your path, but you already did that, and you don't need that second line calling for C:\SNESKey\SNESKey.exe.
Step 2: Find out if your LPT address match's the one in the main sneskey.ini (the one in the SNESKey folder), to find it:
Right click My Computer, select Properties, click the Device Manager tab, double click on Ports, double click on ECP Printer Port (LPTx), click on Resources tab, now look at the Input/Output Range, your looking at the last 3 digits of the first part (e.g., mine is 03BC-03BF, so the only number we need in this example is... 3BC), now add your port address to the main SNESKey.ini file on line 5.
Step 3: Copy one of the .ini files from C:\SNESKey\examaples folder to PJ64's folder (2snes.ini may be the best for you ATM), and rename it to sneskey.ini, you just have to edit the program path in the .ini file (the one in your emulator folder, to something like this ProgPath = C:\emuladores\ninten~1\projec~1\project64.exe) for now, you can latter edit it for the rest of your configurations.
Step 4: Run your batch file.
Step 5: If you passed step 4, PJ64 should load, if it does, configure the input plugin with gamepad one and two, if both gamepads can enter keyboard key's, then edit the SNESKey.ini file in PJ64 folder to your liking, but don't forget to add the other 2 controller's!
If it still doesn't work, attach both the main and the settings .ini files here, so I can look them over :flowers: