I assume this 'complete' tune up was plugs, wires and plennum (intake surge tank) gasket?
If so, recommend you first check to see if you are getting an injector pulse to the #3 injector (a noid light is normally used to verify the injector is receiving the 'pulse' from the ECM. The
noid light is a very useful tool in finding out if you have problems with your fuel injector. It is cheap (around 10 dollars per piece), easy to use (if the light blinks, your injector is receiving the electrical pulse to open). If after you verify the injector pulse is present, the next step is to determine if the injector or cylinder is the problem. A simple verification process requires swapping the #3 injector with another to see if the misfire moves to the swapped cylinder.(.i.e, move #3 injector to #2 cylinder & the #2 injector to #3 cylinder.).. Then run engine to see if the P0303 changes to P0302. This would VERIFY the injector is in some way defective. If the misfire STAYS at #3 cylinder, you'll want to perform a compression test of all the cylinders. If after this test you find #3 cylinder is more than 10% lower than all the other cylinders, do a 'Leak-Down' test to determine if the low compression is due to leaky valves (intake or exhaust) or whether the piston/rings are the problem. NOTE: If all the cylinders are withing 10% of each other during the compression test, the possible causes are, injector O-ring leak, vacuum leak at the intake manifold at #3 cylinder, or the spark plug not firing under compression.