I see a couple of potential problems. Your emitters are not being driven very hard. The mocrocontroller's outputs are not meant to push current. Using a Darlington array (one of the ULN series, like the ULN2803) will let you operate those IRLED's at closer to 50 ma so they are a lot brighter.
Second, your phototransistors turn on when lit and pull the level down. Using a larger resistor in series, like 27K, will let the signal drop closer to ground. At any rate, going to within .1 volt is well within the LOW logic level.
Second, your phototransistors turn on when lit and pull the level down. Using a larger resistor in series, like 27K, will let the signal drop closer to ground. At any rate, going to within .1 volt is well within the LOW logic level.