88 civic with b16a swap missing and surging

It doesn't sound like a mechanical problem. Its probably in the ignition or fuel. I'm willing to bet it is the ignition. Check your distributor, take the cap off and check all the contacts. If everything looks okay and you are still missing, replace the cap and rotor. Replace the spark plug wires and check the spark plugs. Just make sure they're gapped correctly. Hope this helps.