Well, make sure you are at the top of the compression stroke, not the exhaust stroke. If you didn't have a valve cover off and weren't watching the rockers to make sure the intake rocker moves prior to the piston coming up you could have set #1 on the exhaust stroke. It pushes air out of the cylinder on the exhaust stroke too which is why you should visually look at the rockers.
2000 Mustang GT Steeda #0048 34k miles. 99 Cobra 4V swapped, FTBR IRS swapped, exhaust, tuned by James Gordon.
Just because I give you advice, doesn't mean I know more than you. Its just means I've done more stupid ****.