FLT ASSIST RECEIVED BY SMA PLT AS INFLT ENG SHUTDOWN EXECUTED. ALTDEV OCCURS LATER WHEN OTHER ENG IS INADVERTENTLY SHUT DOWN DURING CHKLIST USE BY SPI.

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IFR TRAINING FLT FROM YIP-JXN-YIP. DURING SHORT CRUISE PHASE FROM JXN-YIP (43 MIS) (NO. 1 FRONT) ENG BEGAN RUNNING VERY ROUGH. COULD NOT KEEP ENG RUNNING WITH HIGH BOOST OR MIXTURE CTL. TANK HAD PLENTY OF FUEL; 23 GALLONS; MORE THAN 2 HRS REMAINED. STOPPED ROTATION ON NO. 1; ADVISED ALT AND ASKED FOR A HDG TO YIP AND THE WIND/WX. IN ADDITION; I GAVE THE STUDENT THE ENG FAILURE CHK LIST AND ASKED THAT HE COMPLETE THE 'SECURING ENG' PORTION. WE HAD BRIEFED THIS PROC ON THE GND; BUT HAD NOT COMPLETED THE DRILL IN THE ACFT I WAS BUSY AND FELT THAT I COULD MONITOR HIS ACTIONS AS I FLEW. A GOOD INSTRUCTOR WILL ALLOW A STUDENT TO LEARN FROM ERRORS. MY STUDENT COMPLETED THE SECURING ENG CHK AND SHORTLY AFTER THE NO. 2 ENG LOST PWR. I KNEW THE ENG AND TANK HAD FUEL AND SAID 'GET ME SOME FUEL'. HE HAD COMPLETED THE SECURING CHK LIST BY TURNING THE FUEL SELECTOR FOR THE OPERATIVE (REAR) ENG OFF. IT TOOK ME LESS THAN A MIN TO IDENT AND CORRECT THE PROBLEM. HOWEVER; MY WORKLOAD WAS VERY HIGH AND WE LOST OVER 1000 FT OF ALT IN THE PROCESS. AFTER REGAINING PWR TO THE REAR ENG; I ACCEPTED HDG TO ARB; 6.5 MI TO NE. LNDG WAS UNEVENTFUL. DRAINED THE MAIN SUMPS AND DRAINS ON THE L TANK AND FOUND SIGNIFICANT WATER AND ICE ON THE FUEL (MORE THAN 1/2 GALLON). HAD MAINT COMPLETELY FLUSH AND DRAIN FUEL TANKS. CONTINUED TO FIND WATER AFTER FOUR CYCLES OF FLUSHING THE TANKS. THIS ACFT IS IN VERY GOOD MECHANICAL CONDITION; HOWEVER; THE OWNER HAS IT OUTSIDE. I SUSPECT THIS ACFT HAS HAD FUEL CONTAMINATION FOR SOME TIME. I DRAINED FUEL FROM AUX AND MAIN SUMPS EARLIER IN THE DAY WITH NO SIGNIFICANT CONTAMINATION. THE EFFECT OF FLYING 4 HRS THIS DAY IN VERY COLD TEMPERATURES EXPOSED THE TRUE PROBLEM.