Are you starting it before checking it after the oil and filter change? And 5 quarts would over fill it by slightly more than half a quart. On a side note, all Hondas from '06 to 'til present are factory filled with at least a synthetic blend oil. Personally I wouldn't trust conventional oil...
First of all, you're going entirely too long on conventional motor oil. I'm surprised it was ONLY less than a quart low. Less than 5 quarts in your crankcase technically doesn't read on the dipstick even though there's some at the end. Does your rear main seal leak. It's a very common problem...
It's definitely Mercon V. Mercon SP wasn't factory filled in a Ford Transmission until '06 or '07 let alone even developed for the '04 year. Just get some ATF and a good shudder guard that makes AF3 meet Mercon V specs unless you actually want to go synthetic which is just better anyway. And...