So my 2000 civic EX was running fine when I left my house but then about 5 miles down the road the engine check light starts flashing. I took it to autozone and they gave me the code P1399. It says it's a misfire that could be caused by a clogged EGR valve or a clearance issue on the valve...

I'm horrible at locating EGR valves and can't find mine on my engine? The shop manual didn't seem to help either cause my dad says it shouldn't be located on the intake manifold??? Sooo where is it? Thanks!

 

Unless it's a California model, it won't have an EGR system. Thus no EGR valve.

You should adjust the valve clearance and consider replacing the tune-up parts that usually cause misfiring -- plugs, wires, cap, rotor. Also check for vacuum leaks around the intake.