Need help diagnosing a misfire on my 07 wrangler! Back story: I bought this jk from a junkyard with a hole in the block, I rebuilt a 3.8 and tossed it in. I've been struggling to get it running half decent, it started off with cylinder 2 and 5 not getting spark, so I replaced the Coil and it's been running okay since. As I drive it, it hiccups idling but drives okay around town. The biggest issue is on the freeway or highway between 1500 - 2000rpm with light to medium throttle it starts missing so bad and even pops and bangs like its backfiring through the intake or in the exhaust. If I give it more throttle and it downshifts it drives okay and smoothes out a bit but obviously is down on power. It will rev through the RPM range fine and has excellent throttle response. The only codes I get are downstream o2 on bank 2, misfire on cylinder 6, and recently just got p0404 exhaust gas recirculation performance. I've cleaned the injectorsreplaced the injectors and fuel railReplaced Ignition coilReplaced spark plugs and wiresDid a compression test and all cylinders are 150-160 psiDid a fuel pressure test 50-60 psi idling and under load, and doesn't leak down afterChecked plugs and wiring to Coil and injectorsTested for continuity and shorts to ground between Ignition coil plug and ecm When I do accelerate and it downshifts, the check engine light will pop on and, ding, and flash for a couple seconds then ding and turn off. Any insight or advice is appreciated!

 

I have noticed on injector purchase. they say 3.8 but when you look at the year it fits, they only start at 2010 must be some difference. in early models. maybe someone can shed light on this. might be your issue.