I solved the file problem like this:
    function base64ToFile(base64Data, tempfilename, contentType) {
    contentType = contentType || '';
    var sliceSize = 1024;
    var byteCharacters = atob(base64Data);
    var bytesLength = byteCharacters.length;
    var slicesCount = Math.ceil(bytesLength / sliceSize);
    var byteArrays = new Array(slicesCount);
    for (var sliceIndex = 0; sliceIndex < slicesCount; ++sliceIndex) {
        var begin = sliceIndex * sliceSize;
        var end = Math.min(begin + sliceSize, bytesLength);
        var bytes = new Array(end - begin);
        for (var offset = begin, i = 0 ; offset < end; ++i, ++offset) {
            bytes[i] = byteCharacters[offset].charCodeAt(0);
        }
        byteArrays[sliceIndex] = new Uint8Array(bytes);
    }
    var file = new File(byteArrays, tempfilename, { type: contentType });
    return file;
}
Next problem is the format that angular-file-upload is reading the file in..