Just picked up a 2000 mustang for $800. Runs good but the check engine light is flashing what could be causing that

 

You've already answered your own question with your thread header...Engine misfire.

What you need to do is connect an OBDII code reader to see which cylinder(s) are missing.

You do not want to drive an engine with a misfire so bad it blinks the CEL. You'll cook the catalytic converters from all of the unburnt fuel being sent to them. The fuel will cause the cats to glow red. A Cali vehicle (V6?) is hella expensive to buy the cats for since there are two precats and two cats (four all together).

 

Started to say "If he has CATs " then saw the location. Cant do anything in that strange state.

 

check the following:

make sure all fuel injectors are connected well and not loose (loose injectors or bad ones will cause a misfire and flashing engine light)

replace spark plugs and wires with new ones (what way you know you have a good set). Also make sure they are in the correct firing order. the 1 and 5 cylinder are towards the front, the 3 and 4 are towards the rear of car.

1 2 3 passenger side

5 6 4 driver side


coil pack may also be bad as well

possible leak in piston chambers. do a compression test and make sure valves are good.

hopefully that will get you started. I hope its something simple
Good luck!