Ok, so I figured it out.
Imagick was the way to go, and my use of it was good. I just goofed up on the file name because I wasn't using a proper dynamic variable name. Code should have looked like this:
CODE
$imageBlob = base64_decode((string)$pdf->PDFBytes);
${'imagick'.$x} = new Imagick();
${'imagick'.$x}->readImageBlob($imageBlob);
${'imagick'.$x}->setImageFormat('jpeg');
${'imagick'.$x}->setImageCompressionQuality(60);
${'imagick'.$x}->adaptiveResizeImage(1024,768,true);
$imageBlob = ${'imagick'.$x}->getImageBlob();
$PDFdata[] = base64_encode($imageBlob);
$PDFfile[] = $FormCustomField . $x . '.jpg';
So the error I was getting was because of an invalid file name, because the $x variable in the previous code was getting junk values. Now everything works fine.