<aura:registerEvent name="linkEvent" type="c:MyLinkEvent" />
//
buildComponent:function(component, options) {
    $A.createComponent('InputComp', options, function(el) {
        var body = component.get('v.body');
        if (options['link']) {
            el.addEventHandler('linkEvent', el.getReference('c.handler'));
        }
        body.push(el);
        component.set('v.body', body);
    });
},
handleComponentEvent:function(component, event, helper) {
    var val = event.getParam('payload');
    var link = event.getParam('link');
    // Do some things
    var ev = component.getEvent('linkEvent');
    ev.setParams({'payload':val,'link':link});
    ev.fire();
}

<aura:registerEvent name="linkEvent" type="c:MyLinkEvent" />
//
handler:function(component, event) {
    console.log('This is not being logged');
    var eLink = event.getParam('link');
    var cLink = component.get('v.link');
    if (eLink==cLink) {
        // Do some things
    }
}