Just a question but how did you check the cap,wires and rotor? it sounds like the plug is not firing. you mentioned #1 and #2 cylinders are missfiring. if thats true thoes are not compainon cylinders because they are on different banks. I think you mean #1 and #3 cylinder. Have you swapped plugs and wires with other cylinders? I would do that before you replace injectors. And on that note, you could switch your injector location and see if the miss follows the old injector.
Have you looked in to the EGR valve? If that is not closing properly it will cause idle issues, but "dissapear" above idle.
it could be a compression issue, but you could pull the PVC and see if its breathing heavy/ have a lot of blow by. if you do the compression test, puta couple squirts oil down the cylinder to see if it seals.