I have a 2000 Monte Carlo LS, 3.4. I just completed a head gasket job and I have a misfire on cylinders 4 and 5. As I rev the engine and watch the scan tool, cylinder 4 stops misfiring at 2000 rpm and once I get to 3000 rpm then cylinder 5 stops misfiring. I had the heads rebuilt by a trustworthy engine shop, valve job and milled. I torqued all bolts to spec. Engine has 180 psi on all cylinders. It ran fine before I took it apart aside from a cylinder 2 misfire at start up due to a bad head gasket. I've switched plugs, wires, coil and module. It has 15-16 inches of vacuum at idle. I'm at a loss as to what the problem may be. Hoping it's something simple and someone here can lead me in the right direction

 

First thing I would do before swapping any parts is double check the firing order. Make sure you don't have plug wires mixed up, since you are getting codes specific to cylinders #4 and #5, would double check those are correct.

 

Yes I have checked the firing order several times

 

I figured out why cylinder 5 was misfiring. The ground electrode on the spark plug got smashed down onto the center electrode. I put all new plugs in. Still have a miss on cylinder 4 but only at idle. I do recall as I put it all back together that one fuel injector was missing a piece of plastic at the very tip. I can't remember if it was the #4 injector or not or if it matters. I figured as long as I replaced the o rings that it would be fine

 

That cap on the injector is referred to as a pintle cap. I cannot recall if that alters the spray pattern of the injector. If it does, then you do need that. It *might* just server as a way to hold the o-ring in place. Just for giggles, get a can of starting fluid. With the engine running, try spraying a mist of starting fluid around the #4 injector (which I know is not the easiest task with that upper intake covering them), see if the idle changes as a result. If so, then you might have a bad seal on that injector. Another item, with the car running, I think there is a big connector for the harness that goes to each injector. Disconnect that harness and ohm check each injector via the connector for the harness. You are looking to see if their is an open on #4 OR a noticeable resistance difference with #4 vs all the rest.