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Hey guys Ruben here in Phoenix Arizona. If you wouldn't mind quick entertaining taking the leakdown tester on both cylinder 1 and 3 individually and cranking up the pressure to a good 80 to 100PSI and watch for bubbles and any air coming thru cooling system reservoir. It sounds to me like you have coolant leak into these two cylinders especially with them be right next to each other. If you bring that cylinder to TDC and crank up some pressure with the leak down tester you will more then likely see air coming thru the cooling system which means your diagnostics are done my friend.
This rather silly test has nailed down a few of those misfires that just take up so much time. Please keep me posted but I think this may give you some insight
I have found this to be the problem on not only GM but also a few acuras and one Nissan too. Its one of the most sneaky misfires to misdiagnose. Nut super easy to nail it with 100 percent certainty