[buzzinhalfdozen]

Sorry didn't see you had replaced cap. Have you looked to see what your camshaft retard is? This is the degrees the cam sensor triggers at, if it's off you can move the dist. just like setting timing and set to 0 degrees... you must rev the engine to over 1000 rpms after adjustment to read the new setting. Could be the rotor phase is off and you're getting spark cross in the cap. Kind of a long shot but easy to check and adjust, just seems odd that it's those 2 cyls having miss fires since there not in direct relation to each other. Mark is correct that installing the nozzles in the wrong hole will cause a miss though hard to believe they could have crossed nozzles to other bank. Have you performed an injector balance test yet, if not it may tell you something, not sure if the scanner you're using has this as a special function or not. Typically "harsh" misfires are Ignition related where "subtle" rough idle are more fuel related in my experience. Joe