ACFT EQUIP PROB ALTDEV ALT OVERSHOT - PLT NOTICED THAT THE R ENG WAS RUNNING ROUGH JUST AFTER TKOF AND OVERSHOT ALT WHILE TROUBLE-SHOOTING.

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DEPARTED DET AT XA00 LCL. DEPARTING RWY 33. APPROX 500 FT AGL NOTICED MINOR ROUGHNESS IN R ENG; AND INABILITY TO SYNCHRONIZE PROPS. CONTINUED CLBOUT TO 5000 FT MSL. DURING CLB; ATTEMPTED TO DETERMINE CAUSE OF ROUGHNESS. TURNED OFF R MAGNETO ON R ENG; ROUGHNESS INCREASED. TURNED BACK ON R MAGNETO; TURNED OFF L MAGNETO; ENG RAN SMOOTHLY. DECIDED TO CONTINUE FLT. DURING LEVELOFF; ATC ASKED IF ACFT WAS LEVEL AT 5000 FT. ACFT WAS LEVEL AT 5000 FT; HOWEVER XPONDER WAS INDICATING HIGHER. XPONDER THEN LOST MODE C CAPABILITY FOR APPROX 10 MINS. R ENG CONTINUED TO RUN SMOOTHLY ENRTE TO OSV. CANCELED IFR AND PROCEEDED VFR AT 6500 FT WITH ADVISORIES. NEARING S SHORELINE OF LAKE ERIE; R ENG RAN ROUGH AGAIN. DECIDED TO DIVERT TO TOLEDO EXPRESS; LANDED AT TOLEDO EXPRESS WITHOUT FURTHER INCIDENT. AT THIS TIME OF WRITING; UNSURE OF MECHANICAL PROBS WITH R ENG. HUMAN PERFORMANCE CONSIDERATIONS: XPONDER PROB DELAYED TROUBLE-SHOOTING OF ENG; SHOULD HAVE GIVEN MORE PRIORITY TO ENG AND ADVISED DETROIT ATC OF PROB. DECISION TO CONTINUE FLT WAS QUESTIONABLE; HOWEVER ACFT WAS RUNNING SMOOTHLY. WAS TOO PREOCCUPIED WITH ENG; DID NOT EXECUTE NORMAL CHKLIST PROCS TO PERSONAL STANDARDS.