Try this code
Qualtrics.SurveyEngine.addOnload(function ()
{
    var header = document.createElement("div");
    header.className = "header"
    header.id = "header_1";


    var timer = document.createElement("div");
    timer.className = "timer";
    timer.id = "timer_1";
    timer.innerHTML = "Time Remaining: 00:00:10";


    header.appendChild(timer);
    document.body.insertBefore(header, document.body.firstChild);


    function startTimer(duration, display) {
        var timer = duration, hours, minutes, seconds;
        var myTimer = setInterval(function () {
            Qualtrics.SurveyEngine.setEmbeddedData('timeRemaining', timer);
            hours = Math.floor(timer / 3600);
            timer %= 3600;
            minutes = Math.floor(timer / 60);
            seconds = timer % 60;
            hours = hours < 10 ? "0" + hours : hours;
            minutes = minutes < 10 ? "0" + minutes : minutes;
            seconds = seconds < 10 ? "0" + seconds : seconds;
            var text = ('innerText' in display) ? 'innerText' : 'textContent';
            displayttext] = hours + ":" + minutes + ":" + seconds;


            if (--timer < 0) {
                clearInterval(myTimer);
                timeOver();
            }
        }, 1000);
    }
    var timerSeconds = parseInt("${e://Field/timeRemaining}");
    display = document.querySelector('#time');
    startTimer(timerSeconds, display);
    var timeOver = function () {
        document.getElementById("timer_1").innerHTML = "Time is up.";
        x = 1;
        var bgColor = setInterval(change, 1000);
        $('NextButton').click();
    }
});

This is the coding we ended up going with. We just put in 105 minutes instead of one hour and 45 minutes. It makes everything work the way we want it except it randomly makes the seconds jump up in milliseconds between each second. It looks like some weird glitch. Any suggestions?