create-public-keys.sh

#!/bin/bash

SSH_PUB_DIR="$HOME/.ssh/pub"
mkdir -p $SSH_PUB_DIR
for PRIVATE in *.pem;
do
    PUBLIC=`echo $PRIVATE | sed 's/\(.*\).pem/\1/'`.pub;
    if [ ! -f "$SSH_PUB_DIR/$PUBLIC" ]
    then
        echo $PRIVATE to $PUBLIC;
        ssh-keygen -y -f $PRIVATE > $SSH_PUB_DIR/$PUBLIC;
    fi
done

Run from ~/.ssh. Then use ssh-add -d ~/.ssh/pub/$KEYNAME.pub to remove an individual key from ssh-agent