I've barely ever done anything with a PE (non-plus), but let me take a stab at a few things:
Are you using the same size coin that the machine originally accepted (ie. not using quarters in a machine originally set up for dollar coins)? If you're using a different size coin, it's possible that the encoder insert isn't pushing the coins across the optics correctly to get them to register.
Also, you'll want to make sure DIP switch 3 (located near the volume pot) is set to "ON" -- that tells the machine that you have coin-in optics, rather than a mechanical switch for coins in.
Finally, according to the manual, the first self test page -- the "SELF TEST - INPUT TEST" screen should display the status of the coin-in optics when they're "activated". Put the machine on that screen, then drop a coin through and/or use a popsicle stick or similar to block and un-block the optics to see if there's any indication on the screen that they're registering.
One last thought: if the coin-in optics are identical to what was used on a PE+, and you have access to a PE+, you could always try putting them into the PE+ and using that self-test input screen to give you a better diagnosis.