What was your compression? It should be about 150 psi with no more than 10% variance. Is it any lower on 3&6? Are you sure it is missing on 3&6? Did someone put it on a scope? Do you feel it when you drive it? or just when it idles?
What did your tuneup consist of? Plugs? Wires? Cap? Rotor? Are you sure you have the wire back in the correct firing order? What about your timing chain. If it is real hard to start and runs with about 1/2 power, the chain may have jumped a tooth.
The only thing the computer does is adjust the carb via the O2 sensor after the engine is warm.
Look down the carb and see if the stepper motor is actuating the 2 metering pins. They should be going back and forth at idle.
Are you sure that when you installed the plugs you didn't get grease on them or some other crud? That will foul things up.
Wish you luck. Keep us posted after you've tried everything. Let us know what the solution is after you fix it too.