What aftermarket lower intakes will match the stock upper?

Do you mean it has the same 5.0 emblem on the top? that is how it mounts on to the intake, if it is the same that would be perfect i haven't thought of the explorer intake. How much $ do those go for?
 
not sure what your intent is, but, the question was 'what lower works with stock upper...'
Holley, or stock are the only options.
An explorer upper/lower will give away the stock look, as they are a dead ringer for a Cobra. A dead give away in my opinion. A good performer, but not stealthy/stock looking.
The Holleys are neat in theory, but port alignment and size on the later castings could well make you pull your hair out.
A stock lower, ported is the economical and stealthy way to go.
I've got over $400 in my stupid Holley lower, and to make a long story short, I am going with a stock lower, worked over by Tom Moss(posted above) here sometime soon... sorry for the delays Tom...

Good luck with your project.