96 Geo Metro 4 Cylinder Running Rough

I have a Metro that my father-in-law has given to me. He told me he had some head work done on it and ever since it has not run right. With the help of my mechanic uncle when he is in town I have determined a few things. What I know is that cylinders 1 & 2 seem to be useless as 3 & 4 are the only ones running. This was determined by plugging and unplugging the wires and listening the the change in the engine. I got a compression gauge and found that all cylinder are registering good compression (3 checks each). They appear to be getting good spark and new plugs do not help. I recently change the intake manifold gasket with no change. Does anyone have ideal on what to try next?

Have you checked the firing order? Are you getting spark at 1 and 2 cylinder? Change the spark plugs, try a new distributor cap, and spark plug wires.

Is it possible that you have a vacuum leak at the intake manifold affecting 1 and 2? Use a vacuum gauge to check the intake vacuum. Squirt carburator cleaner at the intake manifold gaskets and other intake gaskets and hoses to make sure these seals are not leaking (engine will speed up and smooth when you spray a leaking spot). Put a stethiscope on 1 and 2 fuel injectors to see if they a clicking.

Get back to us if these ideas do not pan out.